#@ add de-duplication

#@ filter clusters
EnsemblID = transcript ID
ClusterID = unique ID for the cluster
ReadCount = number of reads that overlap the cluster by at least 1 nucleotide
ModeLocation = coordinate of the location with the highest signal / (signal + background) value
ConversionLocationCount = number of unique location where at least 1 conversion occurred
ConversionEventCount = total number of conversions that occurred within the cluster
NonConversionEventCount = total number of possible conversion events that did not occur
ModeScore = score of the highest signal / (signal + background) value
AvgConversionPct = average conversion % of all conversions in the group containing the cluster
GroupConversionEventCount = number of all conversions in the group containing the cluster
SdevConversionPct = sdev of conversion % of all conversions in the group containing the cluster
MaxConversionPct = max. conversion % of all conversions in the group containing the cluster


conversionFreq = ConversionEventCount / (ConversionEventCount + NonConversionEventCount)
# filter: conversionFreq >0.05 && (ReadCount>=5)

cd /data/results/reference/mmu/mm9/mRNA-genomic-max-intron-15k/
/home/reczko/bin/faToTwoBit mm9-mRNA-introns1k.fa mm9-mRNA-introns1k.2bit


for i in IFN-15mMm.bam
for i in 0hrep3-15mMm1kIntron.bam
for i in 6hrep3-15mMm1kIntron.bam
for i in IGG-15mMm.bam
for i in 2hrep?-15mMm1kIntron.bam
do
    echo $i
    # add MD flags for bowtie format
#    /data/results/tools/samtools/samtools-1.3/samtools calmd -b $i /data/results/reference/mmu/mm9/mRNA-genomic-max-intron-15k/Mus_musculus.NCBIM37.64-toMM9.max-intron-1k  >& /dev/null > foo.bam2
    /data/results/tools/samtools/samtools-1.3/samtools calmd -b $i /data/results/reference/mmu/mm9/mRNA-genomic-max-intron-15k/Mus_musculus.NCBIM37.64-toMM9.tr-with-1k-introns.fa  >& /dev/null > foo.bam2
 samtools view -h foo.bam2  | awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/sam2bowtie.awk  > $i.md.bt
    mv foo.bam2 $i.md.bam
done

#uor
cd /data/images/proton/DKlab/mr/parclip/shrimp-mRNA-introns1k
cat 0hrep1-15mMm.bam.md.bt 0hrep2-15mMm.bam.md.bt 0hrep3-15mMm1kIntron.bam.md.bt > 0h-15mMm1kIntron.bam.md.bt
wc 0h-15mMm1kIntron.bam.md.bt
  222931180  1783449423 29141795018 0h-15mMm1kIntron.bam.md.bt

gcc omit-reads.c -lJudy -o omit-reads
./omit-reads /data/images/proton/DKlab/mr/parclip/shrimp-mRNA-introns1k/0h-15mMm1kIntron.bam.md.bt

# sanity check
head -99999 /data/images/proton/DKlab/mr/parclip/shrimp-genomic-mRNA/IFN-15mMm1kIntron2.bam.md.bt | grep "T>C" | wc
  13530  108240 1690155
]0;/data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1dreczko@max:/data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d$ head -99999 /data/images/proton/DKlab/mr/parclip/shrimp/0hrep1-15mMm.bam.md.bam.bt  | grep "T>C" | wc
  14657  117256 1463303
At
/data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1b/res/recommended_settings_with_sdev
are the clusters with the sdev info added, format:

EnsemblID = transcript ID
ClusterID = unique ID for the cluster
ReadCount = number of reads that overlap the cluster by at least 1 nucleotide
ModeLocation = coordinate of the location with the highest signal / (signal + background) value
ConversionLocationCount = number of unique location where at least 1 conversion occurred
ConversionEventCount = total number of conversions that occurred within the cluster
NonConversionEventCount = total number of possible conversion events that did not occur
ModeScore = score of the highest signal / (signal + background) value
AvgConversionPct = average conversion % of all conversions in the group containing the cluster
GroupConversionEventCount = number of all conversions in the group containing the cluster
SdevConversionPct = sdev of conversion % of all conversions in the group containing the cluster
MaxConversionPct = max. conversion % of all conversions in the group containing the cluster
  
#needed for PARalyzer
cs /data/results/reference/mmu/mm9/mRNA-genomic-max-intron-15k
/home/reczko/bin/faToTwoBit mm9-genomic-mRNA.fa mm9-genomic-mRNA.2bit

/data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/myp-all-1kIntrons2.sh

# paralyzer to bed, more than 5 TtoC
#/data/images/proton/DKlab/mr/parclip/paralyzer/pa2bed-gt5tc.awk 
#in: paralyzer format
#    1      2      3            4           5          6              7           8           9          10                    11                     12
#Chromosome,Strand,ClusterStart,ClusterEnd,ClusterID,ClusterSequence,ReadCount,ModeLocation,ModeScore,ConversionLocationCount,ConversionEventCount,NonConversionEventCount
#out: bed format
#    1      2               3            4    _      5    _     6      _       7    _      8       _           9       _           10                     11        12           
#    1      2               3            4                                                                                                                5         6            
#Chromosome,ClusterStart,ClusterEnd,ClusterID,ClusterSequence,ReadCount,ModeLocation,ConversionLocationCount,ConversionEventCount,NonConversionEventCount,ModeScore,Strand
for i in sh-clusters-*.txt2-1kIntrons.csv
do
    echo $i
    awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/pa2bed-gt5tc.awk $i > $i.bed.gt5tc
done


# /data/images/proton/DKlab/mr/parclip/paralyzer/get-TtoC-conversionPct-noCutoff2.awk adds:
##  1..6(same) AvgConversionPct MaxConversionPct ConversionEventCount SdevConversionPct  
#to dist
# /data/images/proton/DKlab/mr/parclip/paralyzer/pa-dist2bed2.awk
#paralyzer+ format
#Chromosome,Strand,ClusterStart,ClusterEnd,ClusterID,InfoType,AvgConversionPct,MaxConversionPct,ConversionEventCount,SdevConversionPct
#1         ,2     ,3           ,4         ,5        ,6       ,7               ,8               ,9                   ,10
#out: bed format
#    1      2               3            4   _       (7)  _      (9)     _             (10)            5 _               6
#Chromosome,ClusterStart,ClusterEnd,ClusterID,AvgConversionPct,ConversionEventCount,SdevConversionPct, MaxConversionPct ,Strand
for i in sh-distributions-???*.txt2-1kIntrons.csv
 do
 echo $i
 cat $i| awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/get-TtoC-conversionPct-noCutoff2.awk|awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/pa-dist2bed2.awk > $i".avg.csv3.bed"
 done

# intersect maxTtoC_gt_0.25 with clusters
# (note: /data/images/proton/DKlab/mr/parclip/paralyzer/add_conversion_pct2.awk adds
#  AvgConversionPct_ConversionEventCount_SdevConversionPct  MaxConversionPct
# )

#in:
#     1                                                  2        3        4                                                                     5                      6        7                                              8       9        10                             11              12    
#in: ENSMUST00000000254-chr6-+-128884399-128885000	278	324	G5.2_ATTAGTTATTCTATTGGAGTATACAATACTCGAATAGTTCTCAGGCA_275_317_5_96_1643	0.7790820460717197	+	ENSMUST00000000254-chr6-+-128884399-128885000	163	374	G5_0.004717_212_0.019691	0.126365	+

#input 2 parts
#cluster
#    1      2               3            4    _      5    _     6      _       7    _      8       _           9       _           10                     11        12           
#    1      2               3            4                                                                                                                5         6            
#Chromosome,ClusterStart,ClusterEnd,ClusterID,ClusterSequence,ReadCount,ModeLocation,ConversionLocationCount,ConversionEventCount,NonConversionEventCount,ModeScore,Strand
#group/dist
#    1      2               3            4   _       (7)  _      (9)     _             (10)            5                 6
#Chromosome,ClusterStart,ClusterEnd,ClusterID,AvgConversionPct,ConversionEventCount,SdevConversionPct, MaxConversionPct ,Strand

#input all:
#cluster 
#    1      2               3            4    _      5    _     6      _       7    _      8       _           9       _           10                      11        12           
#    1      2               3            4                                                                                                                 5         6            
#Chromosome,ClusterStart,ClusterEnd,ClusterID,ClusterSequence,ReadCount,ModeLocation,ConversionLocationCount,ConversionEventCountC,NonConversionEventCount,ModeScore,Strand
#group/dist
#    7      8            9           10                                                                 11                12
#Chromosome,ClusterStart,ClusterEnd,ClusterID,AvgConversionPct,ConversionEventCountG,SdevConversionPct, MaxConversionPct ,Strand

#out
#Chromosome,ClusterStart,ClusterEnd,ClusterID_ClusterSequence_ReadCount_ModeLocation_ConversionLocationCount_ConversionEventCountC_NonConversionEventCount_ModeScore_AvgConversionPct_ConversionEventCountG_SdevConversionPct, MaxConversionPct ,Strand    


#

bedtools intersect -a  sh-clusters-0hrep1.txt2-1kIntrons.csv.bed.gt5tc  -b sh-distributions-0hrep1.txt2-1kIntrons.csv.avg.csv3.bed -wa -wb -s |awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/add_conversion_pct2.awk > sh-clusters-0hrep1.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2
bedtools intersect -a sh-clusters-2hrep1.txt2-1kIntrons.csv.bed.gt5tc -b sh-distributions-2hrep1.txt2-1kIntrons.csv.avg.csv3.bed -wa -wb -s |awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/add_conversion_pct2.awk> sh-clusters-2hrep1.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2
bedtools intersect -a sh-clusters-6hrep1.txt2-1kIntrons.csv.bed.gt5tc -b sh-distributions-6hrep1.txt2-1kIntrons.csv.avg.csv3.bed -wa -wb -s |awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/add_conversion_pct2.awk> sh-clusters-6hrep1.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2

bedtools intersect -a  sh-clusters-0hrep2.txt2-1kIntrons.csv.bed.gt5tc  -b sh-distributions-0hrep2.txt2-1kIntrons.csv.avg.csv3.bed -wa -wb -s |awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/add_conversion_pct2.awk > sh-clusters-0hrep2.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2
bedtools intersect -a sh-clusters-2hrep2.txt2-1kIntrons.csv.bed.gt5tc -b sh-distributions-2hrep2.txt2-1kIntrons.csv.avg.csv3.bed -wa -wb -s |awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/add_conversion_pct2.awk> sh-clusters-2hrep2.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2
bedtools intersect -a sh-clusters-6hrep2.txt2-1kIntrons.csv.bed.gt5tc -b sh-distributions-6hrep2.txt2-1kIntrons.csv.avg.csv3.bed -wa -wb -s |awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/add_conversion_pct2.awk> sh-clusters-6hrep2.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2

bedtools intersect -a  sh-clusters-0hrep3.txt2-1kIntrons.csv.bed.gt5tc  -b sh-distributions-0hrep3.txt2-1kIntrons.csv.avg.csv3.bed -wa -wb -s |awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/add_conversion_pct2.awk > sh-clusters-0hrep3.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2
bedtools intersect -a sh-clusters-2hrep3.txt2-1kIntrons.csv.bed.gt5tc -b sh-distributions-2hrep3.txt2-1kIntrons.csv.avg.csv3.bed -wa -wb -s |awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/add_conversion_pct2.awk> sh-clusters-2hrep3.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2
bedtools intersect -a sh-clusters-6hrep3.txt2-1kIntrons.csv.bed.gt5tc -b sh-distributions-6hrep3.txt2-1kIntrons.csv.avg.csv3.bed -wa -wb -s |awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/add_conversion_pct2.awk> sh-clusters-6hrep3.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2

bedtools intersect -a sh-clusters-IFN.txt2-1kIntrons.csv.bed.gt5tc -b sh-distributions-IFN.txt2-1kIntrons.csv.avg.csv3.bed -wa -wb -s |awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/add_conversion_pct2.awk> sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2
bedtools intersect -a sh-clusters-IGG.txt2-1kIntrons.csv.bed.gt5tc -b sh-distributions-IGG.txt2-1kIntrons.csv.avg.csv3.bed -wa -wb -s |awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/add_conversion_pct2.awk> sh-clusters-IGG.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2
bedtools intersect -a sh-clusters-IL4.txt2-1kIntrons.csv.bed.gt5tc -b sh-distributions-IL4.txt2-1kIntrons.csv.avg.csv3.bed -wa -wb -s |awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/add_conversion_pct2.awk> sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2

# separate plus strand results
for i in sh-clusters-*1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2
do
    wc $i
    awk -f ../filterPlusStrand.awk $i > $i.plus
    wc !$
done
    754552   4527312 131501428 sh-clusters-0hrep1.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2
  406385  2438310 71003130 sh-clusters-0hrep1.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus
  508797  3052782 88325829 sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2
  275171  1651026 47880004 sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus
  372362  2234172 63783284 sh-clusters-IGG.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2
  200678  1204068 34448891 sh-clusters-IGG.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus
  1118143   6708858 197457040 sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2
   607183   3643098 107466384 sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus

#here
awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/filter_GE5reads_convEvPctGT5.awk sh-clusters-IGG.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus > sh-clusters-IGG.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.f

#remove IGG regions
for i in sh-clusters-*1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus
do
    wc $i    
    bedtools intersect -a $i -b sh-clusters-IGG.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.f -v -s |awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/filter_GE5reads_convEvPctGT5.awk |sort -k1,1 -k2,2n  > $i.noIGG.f
    wc !$
done
   406385  2438310 71003130 sh-clusters-0hrep1.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus
  201014  1206084 34939979 sh-clusters-0hrep1.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f
  230535  1383210 39925141 sh-clusters-0hrep2.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus
  124325   745950 21474386 sh-clusters-0hrep2.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f
   630172   3781032 111461295 sh-clusters-0hrep3.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus
  319033  1914198 56190410 sh-clusters-0hrep3.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f
  248467  1490802 43285179 sh-clusters-2hrep1.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus
  123739   742434 21475080 sh-clusters-2hrep1.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f
  441243  2647458 78017048 sh-clusters-2hrep2.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus
  229227  1375362 40446701 sh-clusters-2hrep2.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f
  381937  2291622 66503792 sh-clusters-2hrep3.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus
  200458  1202748 34728724 sh-clusters-2hrep3.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f
   592162   3552972 103271917 sh-clusters-6hrep1.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus
  285681  1714086 49226781 sh-clusters-6hrep1.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f
  506498  3038988 89275744 sh-clusters-6hrep2.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus
  245419  1472514 43066514 sh-clusters-6hrep2.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f
  240866  1445196 41752395 sh-clusters-6hrep3.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus
  133504   801024 23118415 sh-clusters-6hrep3.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f
  275171  1651026 47880004 sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus
  155189   931134 26941627 sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f
  200678  1204068 34448891 sh-clusters-IGG.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus
0 0 0 sh-clusters-IGG.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f
   607183   3643098 107466384 sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus
  279278  1675668 48690486 sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f

#topuniform=max(which(lp8>0.05)); #highest modscore that is not uniformly distributed
Rscript /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/get_modescore_hist_1kIntrons_f.r
[1] "modscore_cutoff for IFN 0.946 0.0591007877911048"
[1] "modscore_cutoff for IL4 0.96 0.0629382265671651"
[1] "modscore_cutoff for 0h_rep1 0.95 0.225209996303595"
[1] "modscore_cutoff for 0h_rep2 0.946 0.099803290998472"
[1] "modscore_cutoff for 0h_rep3 0.946 0.0616650068898846"
[1] "modscore_cutoff for 2h_rep1 0.961 0.0985282900778099"
[1] "modscore_cutoff for 2h_rep2 0.957 0.113417438308439"
[1] "modscore_cutoff for 2h_rep3 0.941 0.061839882253766"
[1] "modscore_cutoff for 6h_rep1 0.951 0.0611335641354568"
[1] "modscore_cutoff for 6h_rep2 0.952 0.340071518567869"
[1] "modscore_cutoff for 6h_rep3 0.962 0.0690384376905233"

awk -v th=0.945 -f /data/images/proton/DKlab/mr/parclip/paralyzer/filter_modescore1_keep_best.awk /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f > /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt
wc !$
#  21295  127770 3826706 /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt

awk -v th=0.954 -f /data/images/proton/DKlab/mr/parclip/paralyzer/filter_modescore1_keep_best.awk /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f > /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt
wc !$
#  33981  203886 6151118 /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt

awk -v th=0.948 -f /data/images/proton/DKlab/mr/parclip/paralyzer/filter_modescore1_keep_best.awk /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-0hrep1.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f > /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-0hrep1.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt
wc !$
#  24170  145020 4364548 /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-0hrep1.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt
awk -v th=0.946 -f /data/images/proton/DKlab/mr/parclip/paralyzer/filter_modescore1_keep_best.awk /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-0hrep2.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f > /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-0hrep2.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt
wc !$

awk -v th=0.956 -f /data/images/proton/DKlab/mr/parclip/paralyzer/filter_modescore1_keep_best.awk /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-0hrep3.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f > /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-0hrep3.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt
wc !$


awk -v th=0.956 -f /data/images/proton/DKlab/mr/parclip/paralyzer/filter_modescore1_keep_best.awk /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-2hrep1.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f > /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-2hrep1.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt
wc !$
awk -v th=0.936 -f /data/images/proton/DKlab/mr/parclip/paralyzer/filter_modescore1_keep_best.awk /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-2hrep2.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f > /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-2hrep2.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt
wc !$
awk -v th=0.932 -f /data/images/proton/DKlab/mr/parclip/paralyzer/filter_modescore1_keep_best.awk /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-2hrep3.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f > /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-2hrep3.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt
wc !$

awk -v th=0.941 -f /data/images/proton/DKlab/mr/parclip/paralyzer/filter_modescore1_keep_best.awk /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-6hrep1.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f > /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-6hrep1.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt
wc !$
awk -v th=0.937 -f /data/images/proton/DKlab/mr/parclip/paralyzer/filter_modescore1_keep_best.awk /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-6hrep2.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f > /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-6hrep2.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt
wc !$
awk -v th=0.934 -f /data/images/proton/DKlab/mr/parclip/paralyzer/filter_modescore1_keep_best.awk /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-6hrep3.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f > /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-6hrep3.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt
wc !$


#if 0

#2do include introns+cds
# filter protein_coding_genes and add annotation from  /data/results/reference/mmu/mm9/1kIntrons-stranded/Mus_musculus.NCBIM37.64-toMM9.headers
for i in *txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt
do
 awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/pa2annotate-ExonIntron1.awk  $i |sort -k1,1 -k4,4 -k2,2n -k5,5n > $i.anno1.csv
done


#make genomicbed+tracks:
#ENSMUST00000164402-chr2-+-25430951-25435619	3303	3331	G14114.1_CAGTACATCGCGTTCTCGGTACCTCCCAA_23_3332_4_13_118_0.9630921701788632_1.000000_65_0.000000	1.000000	+
# use genomic coords in $1 for mapping
cd /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d
for i in *1kI*f.flt
do
echo $i
awk -f /data/images/proton/DKlab/mr/parclip/shrimp-mRNA-introns1k/tracks/paralyzer2tracks2.awk $i > $i".genomic.bed"
done


cd /data/images/proton/DKlab/mr/parclip/shrimp-mRNA-introns1k/tracks
for i in /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/*genomic.bed
do
ln -s $i
done

#if tracks needed
for i in *genomic.bed
do
echo $i
sort -k1,1 -k2,2n $i | awk -f /data/images/proton/DKlab/mr/parclip/tracks/correct-bed.awk > $i.srt;  /data/results/tools/gbrowser/bedToBigBed $i.srt /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/mm9.chrom.sizes  $i.bb; echo "bigDataUrl=http://genomics-lab.fleming.gr/fleming/DKlab/mr/parclip/tracks/"$i.bb;
done

http://genomics-lab.fleming.gr/cgi-bin/hgTracks?db=mm9&hubUrl=http://genomics-lab.fleming.gr/fleming/DKlab/mr/parclip/shrimp-mRNA-introns1k/tracks/hub.txt
ENSMUST00000100497-chr5---143664794-143668433	1056	1126	G4560.1_TGATAGTTCGCCATGGATGACGATATCGCTGCGCTGGTCGTCGACAACGGCTCCGGCATGTGCAAAGCCGG_20_1094_8_8_68_0.999106697968966_1.000000_113_0.000000	1.000000	+

0hrep1
ENSMUST00000113676-chr5-+-67698194-67698936	425	459	G6588.1_AGGTCTTAGGGCACATCGCGGTGACCCAGGGTGAC_25_460_4_22_109_0.9998667980625998_0.833333_4_0.333333	1.000000	+
ENSMUST00000022142-chr13---101183104-101184631	814	873	G981.1_GCAGAGTTGTGTCCTCTAGTTGTGTCATAGTGATTCAGTCTGAATGTTATATATTGTTTC_14_874_9_14_137_0.9979809824870751_1.000000_60_0.000000	1.000000	+
#diff correct-bed2.awk to  correct-bed.awk 
+: start-1 end-1
-: start-1 end-1


# test tracks version for G.Giagkas
#source:
cd /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/test-tracks
for i in *1kI*flt
do
echo $i
awk -f /data/images/proton/DKlab/mr/parclip/shrimp-mRNA-introns1k/tracks/paralyzer2tracks2.awk $i > $i".genomic.bed"
done
cd /data/images/proton/DKlab/mr/parclip/shrimp-mRNA-introns1k/test-tracks
for i in *genomic.bed
do
echo $i
sort -k1,1 -k2,2n $i | awk -f /data/images/proton/DKlab/mr/parclip/tracks/correct-bed.awk > $i.srt;  /data/results/tools/gbrowser/bedToBigBed $i.srt /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/mm9.chrom.sizes  $i.bb; echo "bigDataUrl=http://genomics-lab.fleming.gr/fleming/DKlab/mr/parclip/tracks/"$i.bb;
done
cd /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/test-tracks

cd /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/test-tracks

./update-hub.sh
http://genomics-lab.fleming.gr/cgi-bin/hgTracks?db=mm9&hubUrl=http://genomics-lab.fleming.gr/fleming/DKlab/mr/parclip/shrimp-mRNA-introns1k/test-tracks/hub.txt
http://genomics-lab.fleming.gr/cgi-bin/hgTracks?udcTimeout=0&db=mm9&hubUrl=http://genomics-lab.fleming.gr/fleming/DKlab/mr/parclip/shrimp-mRNA-introns1k/test-tracks/hub.txt
#endif tracks needed

# outlier removal using MDS+trees: 0hrep1 2hrep3 6hrep3
# intersect clusters after outlier removal
#prepare 2 of 3 intersection
for i in sh*rep*1kIn*f.flt
do
cat $i | sort -k1,1 -k2,2n > $i.srt
done

# sh-clusters-0hrep2.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.srt 
ENSMUST00000170376-chr10---13243648-13244249	268	337	G6665.1_TTGAGTATGATAACTTGTTGCAATAAACTATTTTAATAAAATATAGCTTTGTTTAGTTAATGCTTTTTAG_10_338_5_6_77_0.999817838122349_1.000000_111_0.000000	1.000000	+
# sh-clusters-0hrep3.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.srt
ENSMUST00000170376-chr10---13243648-13244249	240	273	G16315.1_GTATAAATTTAATAACTTTGTATTGATTTTGAGT_21_274_4_8_217_0.9780242797679841_0.708333_4_0.343592	1.000000	+
ENSMUST00000170376-chr10---13243648-13244249	321	351	G16316.1_TAGTTAATGCTTTTTAGCCATTAATTTATTT_28_352_4_10_258_0.9461657648651448_1.000000_120_0.000000	1.000000	+
=> 2 clusters overlapping with 1 larger

bedtools multiinter -i   sh-clusters-0hrep2.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.srt  sh-clusters-0hrep3.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.srt  > sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.intersection-all.bed3-1kIntrons
bedtools multiinter -i sh-clusters-2hrep1.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.srt   sh-clusters-2hrep2.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.srt   > sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.intersection-all.bed3-1kIntrons
bedtools multiinter -i sh-clusters-6hrep1.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.srt   sh-clusters-6hrep2.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.srt   > sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.intersection-all.bed3-1kIntrons

## 2of2
#add paralyzer details to intersection:
awk -v f1="sh-clusters-0hrep2.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.srt" -v f2="sh-clusters-0hrep3.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.srt"  -f ../get-multiintersect-details-2of2.awk  sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.intersection-all.bed3-1kIntrons >  sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.intersection-all.bed3-1kIntrons.bed
awk -v f1="sh-clusters-2hrep1.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.srt" -v f2="sh-clusters-2hrep2.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.srt"  -f ../get-multiintersect-details-2of2.awk  sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.intersection-all.bed3-1kIntrons >  sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.intersection-all.bed3-1kIntrons.bed
awk -v f1="sh-clusters-6hrep1.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.srt" -v f2="sh-clusters-6hrep2.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.srt"  -f ../get-multiintersect-details-2of2.awk  sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.intersection-all.bed3-1kIntrons >  sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.intersection-all.bed3-1kIntrons.bed

#merge book-ended regions:
awk -f ../get-merged-multiintersect-details1.awk sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.intersection-all.bed3-1kIntrons.bed > sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.intersection-all.bed3-1kIntrons.merged.bed
awk -f ../get-merged-multiintersect-details1.awk sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.intersection-all.bed3-1kIntrons.bed > sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.intersection-all.bed3-1kIntrons.merged.bed
awk -f ../get-merged-multiintersect-details1.awk sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.intersection-all.bed3-1kIntrons.bed > sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.intersection-all.bed3-1kIntrons.merged.bed
#get max scoring cluster, add max avgConvPct as score
awk -f ../get-max-intersect-score2.awk  sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.intersection-all.bed3-1kIntrons.merged.bed > sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.intersection-all.bed3-1kIntrons.merged.maxAvg.bed
awk -f ../get-max-intersect-score2.awk  sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.intersection-all.bed3-1kIntrons.merged.bed > sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.intersection-all.bed3-1kIntrons.merged.maxAvg.bed
awk -f ../get-max-intersect-score2.awk  sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.intersection-all.bed3-1kIntrons.merged.bed > sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.intersection-all.bed3-1kIntrons.merged.maxAvg.bed
wc sh-clusters-?h.gt0.25TtoC2.plus.noIGG.f.flt.srt.intersection-all.bed3-1kIntrons.merged.maxAvg.bed
  1641 sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.intersection-all.bed3-1kIntrons.merged.maxAvg.bed
   909 sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.intersection-all.bed3-1kIntrons.merged.maxAvg.bed
  2569 sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.intersection-all.bed3-1kIntrons.merged.maxAvg.bed


## 1of2
#add paralyzer details to intersection:
awk -v f1="sh-clusters-0hrep2.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.srt" -v f2="sh-clusters-0hrep3.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.srt"  -f ../get-multiintersect-details-1of2.awk  sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.intersection-all.bed3-1kIntrons >  sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.bed
awk -v f1="sh-clusters-2hrep1.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.srt" -v f2="sh-clusters-2hrep2.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.srt"  -f ../get-multiintersect-details-1of2.awk  sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.intersection-all.bed3-1kIntrons >  sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.bed
awk -v f1="sh-clusters-6hrep1.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.srt" -v f2="sh-clusters-6hrep2.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.srt"  -f ../get-multiintersect-details-1of2.awk  sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.intersection-all.bed3-1kIntrons >  sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.bed

#merge book-ended regions:
awk -f ../get-merged-multiintersect-details1.awk sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.bed > sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.bed
awk -f ../get-merged-multiintersect-details1.awk sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.bed > sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.bed
awk -f ../get-merged-multiintersect-details1.awk sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.bed > sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.bed
#get max scoring cluster, add max avgConvPct as score
awk -f ../get-max-intersect-score2.awk  sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.bed > sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed
awk -f ../get-max-intersect-score2.awk  sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.bed > sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed
awk -f ../get-max-intersect-score2.awk  sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.bed > sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed
wc -l sh-clusters-?h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed
 57403 sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed
 47320 sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed
 68119 sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed

#endif





# add E/I , PCG anno
for i in  *.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed
do
 awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/pa2annotate-ExonIntron1.awk  $i |sort -k1,1 -k4,4 -k2,2n -k5,5n > $i.anno1.csv
done


#add 5/3utr/cds info:
for i in  *.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed
do
echo $i
awk -f /data/images/proton/DKlab/mr/parclip/shrimp-mRNA-introns1k/tracks/paralyzer2tracks2.awk $i > $i".genomic.bed"
done

grep ENSMUST00000170376 sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.intersection-all.bed3-1kIntrons.merged.maxAvg.bed
ENSMUST00000170376-chr10---13243648-13244249	268	273	G6665.1_TTGAGTATGATAACTTGTTGCAATAAACTATTTTAATAAAATATAGCTTTGTTTAGTTAATGCTTTTTAG_10_338_5_6_77_0.999817838122349_1.000000_111_0.000000_1.000000	1.000000	+
ENSMUST00000170376-chr10---13243648-13244249	321	337	G6665.1_TTGAGTATGATAACTTGTTGCAATAAACTATTTTAATAAAATATAGCTTTGTTTAGTTAATGCTTTTTAG_10_338_5_6_77_0.999817838122349_1.000000_111_0.000000_1.000000	1.000000	+
cluster split due to:
sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.intersection-all.bed3-1kIntrons:ENSMUST00000170376-chr10---13243648-13244249	268	273	2	1,2	1	1
sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.intersection-all.bed3-1kIntrons:ENSMUST00000170376-chr10---13243648-13244249	273	321	1	1	1	0 #gap
sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.intersection-all.bed3-1kIntrons:ENSMUST00000170376-chr10---13243648-13244249	321	337	2	1,2	1	1


for i in *f.flt*.genomic.bed
do
bedtools intersect -a $i -b /data/results/reference/mmu/3utr.bed -wa -wb -s > $i.3utr.bed
wc -l !$
bedtools intersect -a $i -b /data/results/reference/mmu/5utr.bed -wa -wb -s > $i.5utr.bed
wc -l !$
bedtools intersect -a $i -b /data/results/reference/mmu/cds.bed -wa -wb -s > $i.cds.bed
wc -l !$
done

12785 sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.genomic.bed.3utr.bed
3839 sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.genomic.bed.5utr.bed
23560 sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.genomic.bed.cds.bed
5316 sh-clusters-0hrep1.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.genomic.bed.3utr.bed
1284 sh-clusters-0hrep1.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.genomic.bed.5utr.bed
10297 sh-clusters-0hrep1.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.genomic.bed.cds.bed
3315 sh-clusters-0hrep2.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.genomic.bed.3utr.bed
1039 sh-clusters-0hrep2.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.genomic.bed.5utr.bed
6770 sh-clusters-0hrep2.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.genomic.bed.cds.bed
9594 sh-clusters-0hrep3.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.genomic.bed.3utr.bed
2838 sh-clusters-0hrep3.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.genomic.bed.5utr.bed
16959 sh-clusters-0hrep3.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.genomic.bed.cds.bed
10257 sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.genomic.bed.3utr.bed
2243 sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.genomic.bed.5utr.bed
20418 sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.genomic.bed.cds.bed
3080 sh-clusters-2hrep1.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.genomic.bed.3utr.bed
764 sh-clusters-2hrep1.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.genomic.bed.5utr.bed
6840 sh-clusters-2hrep1.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.genomic.bed.cds.bed
7271 sh-clusters-2hrep2.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.genomic.bed.3utr.bed
1498 sh-clusters-2hrep2.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.genomic.bed.5utr.bed
13779 sh-clusters-2hrep2.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.genomic.bed.cds.bed
5473 sh-clusters-2hrep3.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.genomic.bed.3utr.bed
1541 sh-clusters-2hrep3.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.genomic.bed.5utr.bed
11598 sh-clusters-2hrep3.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.genomic.bed.cds.bed
14533 sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.genomic.bed.3utr.bed
4941 sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.genomic.bed.5utr.bed
29803 sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.genomic.bed.cds.bed
7450 sh-clusters-6hrep1.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.genomic.bed.3utr.bed
3270 sh-clusters-6hrep1.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.genomic.bed.5utr.bed
15918 sh-clusters-6hrep1.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.genomic.bed.cds.bed
7340 sh-clusters-6hrep2.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.genomic.bed.3utr.bed
1739 sh-clusters-6hrep2.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.genomic.bed.5utr.bed
14471 sh-clusters-6hrep2.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.genomic.bed.cds.bed
3908 sh-clusters-6hrep3.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.genomic.bed.3utr.bed
1130 sh-clusters-6hrep3.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.genomic.bed.5utr.bed
7944 sh-clusters-6hrep3.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.genomic.bed.cds.bed
4502 sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.genomic.bed.3utr.bed
1406 sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.genomic.bed.5utr.bed
8942 sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.genomic.bed.cds.bed
7059 sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.genomic.bed.3utr.bed
1917 sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.genomic.bed.5utr.bed
14120 sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.genomic.bed.cds.bed

(
# keep matching clusters
for i in  *.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.genomic.bed
do
bedtools intersect -a $i -b /data/results/reference/mmu/3utr.bed -wa -wb -s |awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/keep_matching_clusters.awk > $i.3utr.bed
wc -l !$
bedtools intersect -a $i -b /data/results/reference/mmu/5utr.bed -wa -wb -s |awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/keep_matching_clusters.awk > $i.5utr.bed
wc -l !$
bedtools intersect -a $i -b /data/results/reference/mmu/cds.bed -wa -wb -s |awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/keep_matching_clusters.awk > $i.cds.bed
wc -l !$
done

for i in sh-clusters-I??.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.genomic.bed
do
bedtools intersect -a $i -b /data/results/reference/mmu/3utr.bed -wa -wb -s |awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/keep_matching_clusters.awk > $i.3utr.bed
wc -l !$
bedtools intersect -a $i -b /data/results/reference/mmu/5utr.bed -wa -wb -s |awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/keep_matching_clusters.awk > $i.5utr.bed
wc -l !$
bedtools intersect -a $i -b /data/results/reference/mmu/cds.bed -wa -wb -s |awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/keep_matching_clusters.awk > $i.cds.bed
wc -l !$
done
)

#@ merge bookended clusters
bedtools merge -i A.bed -c 4 -o collapse

ls -lt *srt*.genomic.bed
-rw-r--r-- 1 reczko users 10796967 Jun  1 14:11 sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.genomic.bed
-rw-r--r-- 1 reczko users   294201 Jun  1 14:11 sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.intersection-all.bed3-1kIntrons.merged.maxAvg.bed.genomic.bed
-rw-r--r-- 1 reczko users  7005100 Jun  1 14:11 sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.genomic.bed
-rw-r--r-- 1 reczko users   103642 Jun  1 14:11 sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.intersection-all.bed3-1kIntrons.merged.maxAvg.bed.genomic.bed
-rw-r--r-- 1 reczko users  9545239 Jun  1 14:11 sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.genomic.bed
-rw-r--r-- 1 reczko users   187153 Jun  1 14:11 sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.intersection-all.bed3-1kIntrons.merged.maxAvg.bed.genomic.bed
]0;/data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1dreczko@max:/data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d$ ls -lt *-I??.*.genomic.bed
-rw-r--r-- 1 reczko users 5569621 May 23 12:53 sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.genomic.bed
-rw-r--r-- 1 reczko users 3593977 May 23 12:53 sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.genomic.bed
]0;/data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1dreczko@max:/data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d$  

for i in   *f.flt*.genomic.bed
do
cat $i |sort -k1,1 -k2,2n |bedtools merge -i - -s -c 4,5,6 -o collapse,max,distinct >  foo > $i".collapsed"
done

for i in *f.flt*.genomic.bed.collapsed
do
awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/get-best-collapsed-cluster1.awk $i > $i".best.bed"
done

for i in  *f.flt*.genomic.bed.collapsed.best.bed
do
bedtools intersect -a $i -b /data/results/reference/mmu/3utr.bed -wa -wb -s |sort -k1,1 -k2,2n |bedtools merge -i - -s -c 4,5,6,10 -o distinct,distinct,distinct,collapse  > $i.3utr.bed
wc -l !$
bedtools intersect -a $i -b /data/results/reference/mmu/5utr.bed -wa -wb -s |sort -k1,1 -k2,2n |bedtools merge -i - -s -c 4,5,6,10 -o distinct,distinct,distinct,collapse  > $i.5utr.bed
wc -l !$
bedtools intersect -a $i -b /data/results/reference/mmu/cds.bed -wa -wb -s |sort -k1,1 -k2,2n |bedtools merge -i - -s -c 4,5,6,10 -o distinct,distinct,distinct,collapse > $i.cds.bed
wc -l !$
done


(
bedtools multiinter -i sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.genomic.bed.collapsed.best.bed.3utr.bed sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.genomic.bed.collapsed.best.bed.5utr.bed sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.genomic.bed.collapsed.best.bed.cds.bed > sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.genomic.bed.collapsed.best.3utr.5utr.cds.bed

bedtools multiinter -i sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.genomic.bed.collapsed.best.bed.3utr.bed sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.genomic.bed.collapsed.best.bed.5utr.bed sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.genomic.bed.collapsed.best.bed.cds.bed > sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.genomic.bed.collapsed.best.3utr.5utr.cds.bed

bedtools multiinter -i sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.genomic.bed.collapsed.best.bed.3utr.bed sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.genomic.bed.collapsed.best.bed.5utr.bed sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.genomic.bed.collapsed.best.bed.cds.bed > sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.genomic.bed.collapsed.best.3utr.5utr.cds.bed


bedtools multiinter -i sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.genomic.bed.collapsed.best.bed.3utr.bed sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.genomic.bed.collapsed.best.bed.5utr.bed sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.genomic.bed.collapsed.best.bed.cds.bed > sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.genomic.bed.collapsed.best.3utr.5utr.cds.bed 
bedtools multiinter -i sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.genomic.bed.collapsed.best.bed.3utr.bed sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.genomic.bed.collapsed.best.bed.5utr.bed sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.genomic.bed.collapsed.best.bed.cds.bed > sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.genomic.bed.collapsed.best.3utr.5utr.cds.bed
)

(
awk -v f3="sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.genomic.bed.collapsed.best.bed.3utr.bed" -v f5="sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.genomic.bed.collapsed.best.bed.5utr.bed" -v fc="sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.genomic.bed.collapsed.best.bed.cds.bed"  -f /data/images/proton/DKlab/mr/parclip/paralyzer/per-gene-stats1.awk > sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.genomic.bed.collapsed.best.per-gene.bed 

awk -v f3="sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.genomic.bed.collapsed.best.bed.3utr.bed" -v f5="sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.genomic.bed.collapsed.best.bed.5utr.bed" -v fc="sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.genomic.bed.collapsed.best.bed.cds.bed" -f /data/images/proton/DKlab/mr/parclip/paralyzer/per-gene-stats1.awk > sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.genomic.bed.collapsed.best.per-gene.bed

awk -v f3="sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.genomic.bed.collapsed.best.bed.3utr.bed" -v f5="sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.genomic.bed.collapsed.best.bed.5utr.bed" -v fc="sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.genomic.bed.collapsed.best.bed.cds.bed" -f /data/images/proton/DKlab/mr/parclip/paralyzer/per-gene-stats1.awk > sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.genomic.bed.collapsed.best.per-gene.bed

awk -v f3="sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.genomic.bed.collapsed.best.bed.3utr.bed" -v f5="sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.genomic.bed.collapsed.best.bed.5utr.bed" -v fc="sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.genomic.bed.collapsed.best.bed.cds.bed" -f /data/images/proton/DKlab/mr/parclip/paralyzer/per-gene-stats1.awk > sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.genomic.bed.collapsed.best.per-gene.bed

awk -v f3="sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.genomic.bed.collapsed.best.bed.3utr.bed" -v f5="sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.genomic.bed.collapsed.best.bed.5utr.bed" -v fc="sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.genomic.bed.collapsed.best.bed.cds.bed" -f /data/images/proton/DKlab/mr/parclip/paralyzer/per-gene-stats1.awk > sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.genomic.bed.collapsed.best.per-gene.bed
)

Dear Margarita and George,

the per-gene processing results as discussed are
at
/data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d:
sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.genomic.bed.collapsed.best.per-gene.bed
sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.genomic.bed.collapsed.best.per-gene.bed
sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.genomic.bed.collapsed.best.per-gene.bed
sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.genomic.bed.collapsed.best.per-gene.bed
sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.genomic.bed.collapsed.best.per-gene.bed

0h
6 cds polymorphic_pseudogene
2 5utr IG_V_gene
47 cds IG_V_gene
2 other IG_V_gene 3utr  5utr 2 cds 0
1251 3utr nonsense_mediated_decay
10584 3utr protein_coding
1 cds IG_C_gene
159 5utr nonsense_mediated_decay
2567 5utr protein_coding
648 cds nonsense_mediated_decay
15802 cds protein_coding
156 other nonsense_mediated_decay 1st max: 3utr 114 5utr 42 cds 0 2nd max: 3utr 0 5utr 0 cds 156
1085 other protein_coding 1st max: 3utr 525 5utr 560 cds 0 2nd max: 3utr 0 5utr 2 cds 1083

2h
4 cds polymorphic_pseudogene
23 cds IG_V_gene
2 other IG_V_gene 3utr  5utr 2 cds 0
832 3utr nonsense_mediated_decay
7072 3utr protein_coding
4 cds IG_C_gene
45 5utr nonsense_mediated_decay
1149 5utr protein_coding
390 cds nonsense_mediated_decay
10611 cds protein_coding
86 other nonsense_mediated_decay 1st max: 3utr 74 5utr 12 cds 0 2nd max: 3utr 0 5utr 0 cds 86
576 other protein_coding 1st max: 3utr 310 5utr 266 cds 0 2nd max: 3utr 0 5utr 3 cds 573

6h
2 cds polymorphic_pseudogene
24 cds IG_V_gene
1098 3utr nonsense_mediated_decay
10236 3utr protein_coding
2 cds IG_C_gene
113 5utr nonsense_mediated_decay
2060 5utr protein_coding
542 cds nonsense_mediated_decay
13091 cds protein_coding
138 other nonsense_mediated_decay 1st max: 3utr 105 5utr 33 cds 0 2nd max: 3utr 0 5utr 0 cds 138
849 other protein_coding 1st max: 3utr 437 5utr 412 cds 0 2nd max: 3utr 0 5utr 6 cds 843

IFN
1 3utr IG_V_gene
1 cds polymorphic_pseudogene
10 cds IG_V_gene
383 3utr nonsense_mediated_decay
3532 3utr protein_coding
1 cds IG_C_gene
36 5utr nonsense_mediated_decay
765 5utr protein_coding
197 cds nonsense_mediated_decay
5265 cds protein_coding
48 other nonsense_mediated_decay 1st max: 3utr 36 5utr 12 cds 0 2nd max: 3utr 0 5utr 0 cds 48
325 other protein_coding 1st max: 3utr 129 5utr 196 cds 0 2nd max: 3utr 0 5utr 1 cds 324

IL4
2 cds polymorphic_pseudogene
13 cds IG_V_gene
632 3utr nonsense_mediated_decay
5375 3utr protein_coding
2 cds IG_C_gene
54 5utr nonsense_mediated_decay
982 5utr protein_coding
298 cds nonsense_mediated_decay
7738 cds protein_coding
56 other nonsense_mediated_decay 1st max: 3utr 45 5utr 11 cds 0 2nd max: 3utr 0 5utr 0 cds 56
481 other protein_coding 1st max: 3utr 257 5utr 224 cds 0 2nd max: 3utr 0 5utr 2 cds 479


#@ add intron as categ

# add E/I , PCG anno
for i in  *.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed
do
 echo $i
awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/pa2annotate-ExonIntron2.awk  $i  > $i.anno1.bed
done
for i in sh-clusters-I??.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt
do
 echo $i
 awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/pa2annotate-ExonIntron2.awk  $i  > $i.anno1.bed
done


#@ add de-duplication
for i in  *anno1.bed
do
echo $i
 awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/de-dup-clusters1.awk $i > $i.ded
done

sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed
nmm 150887
57403 17974 31.312 56
sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed
nmm 150887
47320 15135 31.9844 44
sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed
nmm 150887
68119 21519 31.5903 79
sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed
nmm 150887
21295 6741 31.6553 36
sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed
nmm 150887
33981 10860 31.959 33


#get genomic coords, keep anno
for i in  *anno1.bed.ded
do
echo $i
awk -f /data/images/proton/DKlab/mr/parclip/shrimp-mRNA-introns1k/tracks/paralyzer2tracks3.awk $i > $i".genomic2.bed"
done

#bookend merge
for i in   *.anno1.bed.ded.genomic2.bed
do
cat $i |sort -k1,1 -k2,2n |bedtools merge -i - -s -c 4,5,6,7,8,9 -o collapse,max,distinct,collapse,collapse,collapse >  foo > $i".collapsed"
done

#assign exon vs intron based on majority, exon for ties
for i in  *.anno1.bed.ded.genomic2.bed.collapsed
do
awk -f ../per-gene-exon-intron-stats1a.awk  $i > $i.exon-intron
done
# double gene anno for same region in exon-intron.log3, manual check of >5 pairs = > no exon/intron assignment conflict


# get best cluster in collapsed
for i in  *.anno1.bed.ded.genomic2.bed.collapsed
do
awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/get-best-collapsed-cluster2.awk $i > $i".best.bed"
done

# intersect exon-intron-anno with transcript clusters
for i in  *.anno1.bed.ded.genomic2.bed.collapsed
do
#bedtools intersect -a  $i.exon-intron -b $i.best.bed -wa -wb -s  > $i.anno2
bedtools intersect -a  $i.exon-intron -b $i.best.bed -wa -wb -s |awk 'BEGIN{OFS="\t"}{print $8,$9,$10,$11,$12,$13,$14,$7}' > $i.anno2
#bedtools intersect -a  $i.exon-intron -b $i.best.bed -wa -wb -s |awk 'BEGIN{OFS="\t"}{print $8,$9,$10,$11,$12,$13,$14,$7}' > $i.anno2
done

for i in  *.anno1.bed.ded.genomic2.bed.collapsed.anno2
do
awk '{if ($NF=="E"){print $0}}' $i > $i.exon
done

for i in  *.anno1.bed.ded.genomic2.bed.collapsed.anno2
do
awk '{if ($NF=="I"){print $0}}' $i > $i.intron
wc -l !$
#awk '{if ($NF=="I"){print $0}}' $i|sort -k1,1 -k2,2n |bedtools merge -i - -s -c 4,5,6,7,8 -o collapse,collapse,collapse,collapse,collapse  > $i.intron 
#wc !$ #same
done
36739 sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.ded.genomic2.bed.collapsed.anno2.intron
30582 sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.ded.genomic2.bed.collapsed.anno2.intron
43077 sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.ded.genomic2.bed.collapsed.anno2.intron
13621 sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.ded.genomic2.bed.collapsed.anno2.intron
21801 sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.ded.genomic2.bed.collapsed.anno2.intron
(for i in  *anno2
do
bedtools intersect -a $i -b /data/results/reference/mmu/3utr.bed -wa -u -s |sort -k1,1 -k2,2n |bedtools merge -i - -s -c 4,5,6,7,8 -o collapse,collapse,collapse,collapse,collapse  > $i.3utr.bed
wc -l !$
bedtools intersect -a $i -b /data/results/reference/mmu/5utr.bed -wa -u -s |sort -k1,1 -k2,2n |bedtools merge -i - -s -c 4,5,6,7,8 -o collapse,collapse,collapse,collapse,collapse  > $i.5utr.bed
wc -l !$
bedtools intersect -a $i -b /data/results/reference/mmu/cds.bed -wa -u -s |sort -k1,1 -k2,2n |bedtools merge -i - -s -c 4,5,6,7,8 -o collapse,collapse,collapse,collapse,collapse > $i.cds.bed
wc -l !$
done
)

for i in  *.anno1.bed.ded.genomic2.bed.collapsed.anno2.exon
do
bedtools intersect -a $i -b /data/results/reference/mmu/3utr.bed -wa -u -s |sort -k1,1 -k2,2n > $i.3utr.bed
wc -l !$
bedtools intersect -a $i -b /data/results/reference/mmu/5utr.bed -wa -u -s |sort -k1,1 -k2,2n > $i.5utr.bed
wc -l !$
bedtools intersect -a $i -b /data/results/reference/mmu/cds.bed -wa -u -s |sort -k1,1 -k2,2n  > $i.cds.bed
wc -l !$
done

for i in  *.anno1.bed.ded.genomic2.bed.collapsed.anno2.exon
do
bedtools intersect -v -a $i -b   /data/results/reference/mmu/cds.bed /data/results/reference/mmu/5utr.bed /data/results/reference/mmu/3utr.bed -wa  -s |sort -k1,1 -k2,2n  > $i.ncRNA
wc -l !$
done
3633 sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.ded.genomic2.bed.collapsed.anno2.exon.ncRNA
3071 sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.ded.genomic2.bed.collapsed.anno2.exon.ncRNA
4274 sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.ded.genomic2.bed.collapsed.anno2.exon.ncRNA
1348 sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.ded.genomic2.bed.collapsed.anno2.exon.ncRNA
2191 sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.ded.genomic2.bed.collapsed.anno2.exon.ncRNA

awk -v f3="sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.ded.genomic2.bed.collapsed.anno2.exon.3utr.bed" -v f5="sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.ded.genomic2.bed.collapsed.anno2.exon.5utr.bed" -v fc="sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.ded.genomic2.bed.collapsed.anno2.exon.cds.bed"  -f /data/images/proton/DKlab/mr/parclip/paralyzer/per-gene-exon-intron-stats1.awk > sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.ded.genomic2.bed.collapsed.best.per-gene-exons.bed 

awk -v f3="sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.ded.genomic2.bed.collapsed.anno2.exon.3utr.bed" -v f5="sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.ded.genomic2.bed.collapsed.anno2.exon.5utr.bed" -v fc="sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.ded.genomic2.bed.collapsed.anno2.exon.cds.bed" -f /data/images/proton/DKlab/mr/parclip/paralyzer/per-gene-exon-intron-stats1.awk > sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.ded.genomic2.bed.collapsed.best.per-gene-exons.bed

awk -v f3="sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.ded.genomic2.bed.collapsed.anno2.exon.3utr.bed" -v f5="sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.ded.genomic2.bed.collapsed.anno2.exon.5utr.bed" -v fc="sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.ded.genomic2.bed.collapsed.anno2.exon.cds.bed" -f /data/images/proton/DKlab/mr/parclip/paralyzer/per-gene-exon-intron-stats1.awk > sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.ded.genomic2.bed.collapsed.best.per-gene-exons.bed

awk -v f3="sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.ded.genomic2.bed.collapsed.anno2.exon.3utr.bed" -v f5="sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.ded.genomic2.bed.collapsed.anno2.exon.5utr.bed" -v fc="sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.ded.genomic2.bed.collapsed.anno2.exon.cds.bed" -f /data/images/proton/DKlab/mr/parclip/paralyzer/per-gene-exon-intron-stats1.awk > sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.ded.genomic2.bed.collapsed.best.per-gene-exons.bed

awk -v f3="sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.ded.genomic2.bed.collapsed.anno2.exon.3utr.bed" -v f5="sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.ded.genomic2.bed.collapsed.anno2.exon.5utr.bed" -v fc="sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.ded.genomic2.bed.collapsed.anno2.exon.cds.bed" -f /data/images/proton/DKlab/mr/parclip/paralyzer/per-gene-exon-intron-stats1.awk > sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.ded.genomic2.bed.collapsed.best.per-gene-exons.bed

#@
add 2nd class 'horizontal' annotation 3/5/cds/introns

for i in *f.flt.*anno1.bed.ded.genomic2.bed.collapsed.best.per-gene-exons.bed
do
bedtools intersect -a $i -b /data/results/reference/mmu/3utr.bed -wa -u -s |sort -k1,1 -k2,2n > $i.3utr.bed
wc -l !$
bedtools intersect -a $i -b /data/results/reference/mmu/5utr.bed -wa -u -s |sort -k1,1 -k2,2n > $i.5utr.bed
wc -l !$
bedtools intersect -a $i -b /data/results/reference/mmu/cds.bed -wa -u -s |sort -k1,1 -k2,2n  > $i.cds.bed
wc -l !$
bedtools intersect -a $i -b /data/results/reference/mmu/intron.bed -wa -u -s |sort -k1,1 -k2,2n > $i.intron.bed
wc -l !$
done
10995 sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.ded.genomic2.bed.collapsed.best.per-gene-exons.bed.3utr.bed
2230 sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.ded.genomic2.bed.collapsed.best.per-gene-exons.bed.5utr.bed
10568 sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.ded.genomic2.bed.collapsed.best.per-gene-exons.bed.cds.bed
7777 sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.ded.genomic2.bed.collapsed.best.per-gene-exons.bed.3utr.bed
1266 sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.ded.genomic2.bed.collapsed.best.per-gene-exons.bed.5utr.bed
8460 sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.ded.genomic2.bed.collapsed.best.per-gene-exons.bed.cds.bed
11643 sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.ded.genomic2.bed.collapsed.best.per-gene-exons.bed.3utr.bed
2845 sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.ded.genomic2.bed.collapsed.best.per-gene-exons.bed.5utr.bed
13144 sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.ded.genomic2.bed.collapsed.best.per-gene-exons.bed.cds.bed
3477 sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.ded.genomic2.bed.collapsed.best.per-gene-exons.bed.3utr.bed
798 sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.ded.genomic2.bed.collapsed.best.per-gene-exons.bed.5utr.bed
3965 sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.ded.genomic2.bed.collapsed.best.per-gene-exons.bed.cds.bed
5927 sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.ded.genomic2.bed.collapsed.best.per-gene-exons.bed.3utr.bed
1117 sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.ded.genomic2.bed.collapsed.best.per-gene-exons.bed.5utr.bed
6657 sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.ded.genomic2.bed.collapsed.best.per-gene-exons.bed.cds.bed


for i in *f.flt*.anno1.bed.ded.genomic2.bed.collapsed.anno2.exon.ncRNA
do
bedtools intersect -a $i -b /data/results/reference/mmu/3utr.bed -wa -u -s |sort -k1,1 -k2,2n > $i.3utr.bed
wc -l !$
bedtools intersect -a $i -b /data/results/reference/mmu/5utr.bed -wa -u -s |sort -k1,1 -k2,2n > $i.5utr.bed
wc -l !$
bedtools intersect -a $i -b /data/results/reference/mmu/cds.bed -wa -u -s |sort -k1,1 -k2,2n  > $i.cds.bed
wc -l !$
bedtools intersect -a $i -b /data/results/reference/mmu/intron.bed -wa -u -s |sort -k1,1 -k2,2n > $i.intron.bed
wc -l !$
done
#all zero, as expected

for i in *f.flt*.anno1.bed.ded.genomic2.bed.collapsed.anno2.intron
do
bedtools intersect -a $i -b /data/results/reference/mmu/3utr.bed -wa -u -s |sort -k1,1 -k2,2n > $i.3utr.bed
wc -l !$
bedtools intersect -a $i -b /data/results/reference/mmu/5utr.bed -wa -u -s |sort -k1,1 -k2,2n > $i.5utr.bed
wc -l !$
bedtools intersect -a $i -b /data/results/reference/mmu/cds.bed -wa -u -s |sort -k1,1 -k2,2n  > $i.cds.bed
wc -l !$
done
447 sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.ded.genomic2.bed.collapsed.anno2.intron.3utr.bed
501 sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.ded.genomic2.bed.collapsed.anno2.intron.5utr.bed
3198 sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.ded.genomic2.bed.collapsed.anno2.intron.cds.bed
384 sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.ded.genomic2.bed.collapsed.anno2.intron.3utr.bed
406 sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.ded.genomic2.bed.collapsed.anno2.intron.5utr.bed
2783 sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.ded.genomic2.bed.collapsed.anno2.intron.cds.bed
468 sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.ded.genomic2.bed.collapsed.anno2.intron.3utr.bed
588 sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.ded.genomic2.bed.collapsed.anno2.intron.5utr.bed
3634 sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.ded.genomic2.bed.collapsed.anno2.intron.cds.bed
124 sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.ded.genomic2.bed.collapsed.anno2.intron.3utr.bed
178 sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.ded.genomic2.bed.collapsed.anno2.intron.5utr.bed
974 sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.ded.genomic2.bed.collapsed.anno2.intron.cds.bed
215 sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.ded.genomic2.bed.collapsed.anno2.intron.3utr.bed
253 sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.ded.genomic2.bed.collapsed.anno2.intron.5utr.bed
1480 sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.ded.genomic2.bed.collapsed.anno2.intron.cds.bed