#@ 11102018

# adapter removal and quality filtering:

# 86.9% of reads pass at q10 (84.9% nts)
Command line parameters: -q 10 -z -m 15 -c -a CGCCTTGGCCGTACAGCAG IL4/ugc_604_11_F3.csfasta IL4/ugc_604_11_F3.QV.qual
Total reads processed:              13,338,085
Reads with adapters:                 1,992,633 (14.9%)
Reads that were too short:           1,747,909 (13.1%)
Reads written (passing filters):    11,590,176 (86.9%)
Total basepairs processed:   666,904,250 bp
Quality-trimmed:              12,129,910 bp (1.8%)
Total written (filtered):    566,492,252 bp (84.9%)

# 83.9% of reads pass at q20 (60.3% nts)
Command line parameters: -q 20 -z -m 15 -c -a CGCCTTGGCCGTACAGCAG IL4/ugc_604_11_F3.csfasta IL4/ugc_604_11_F3.QV.qual
Total reads processed:              13,338,085
Reads with adapters:                 1,984,803 (14.9%)
Reads that were too short:           2,147,829 (16.1%)
Reads written (passing filters):    11,190,256 (83.9%)

Total basepairs processed:   666,904,250 bp
Quality-trimmed:             192,751,267 bp (28.9%)
Total written (filtered):    402,450,297 bp (60.3%)

# 40.9% of reads pass at q25 (24.7% nts)
Command line parameters: -q 25 -z -m 15 -c -a CGCCTTGGCCGTACAGCAG IL4/ugc_604_11_F3.csfasta IL4/ugc_604_11_F3.QV.qual
Total reads processed:              13,338,085
Reads with adapters:                 2,363,404 (17.7%)
Reads that were too short:           7,881,700 (59.1%)
Reads written (passing filters):     5,456,385 (40.9%)
Total basepairs processed:   666,904,250 bp
Quality-trimmed:             422,345,014 bp (63.3%)
Total written (filtered):    164,427,255 bp (24.7%)

# only 3% of reads pass at q30 (2.2 nts)
Command line parameters: -q 30 -z -m 15 -c -a CGCCTTGGCCGTACAGCAG IL4/ugc_604_11_F3.csfasta IL4/ugc_604_11_F3.QV.qual
Total reads processed:              13,338,085
Reads with adapters:                   577,467 (4.3%)
Reads that were too short:          12,941,228 (97.0%)
Reads written (passing filters):       396,857 (3.0%)
Total basepairs processed:   666,904,250 bp
Quality-trimmed:             617,190,712 bp (92.5%)
Total written (filtered):     14,532,502 bp (2.2%)

# mismatch statistics

#q10
awk -f ../get-mm-stats3.awk IL4-q10-m15-15mMm1kIntron.bam.md.bt
nreads 115828442
nmm 35945140
avgmm 0.310331
0 86974535
1 22649363
2 5424146
3 681848
4 91207
5 6957
6 374
7 12
A>C 3147712 8.75699
A>G 3123805 8.69048
A>T 3137240 8.72786
C>A 2651405 7.37625
C>G 2727225 7.58719
C>T 2459132 6.84135
G>A 2811293 7.82107
G>C 3021430 8.40567
G>T 2780695 7.73594
N>A 2 5.56403e-06
N>C 5 1.39101e-05
N>G 1 2.78202e-06
N>N 1 2.78202e-06
N>T 7 1.94741e-05
T>A 3272500 9.10415
T>C 3476903 9.6728
T>G 3335784 9.28021
max 1mm
A>C 1957027 5.44448
A>G 1995286 5.55092
A>T 1986074 5.52529
C>A 1661982 4.62366
C>G 1712783 4.76499
C>T 1541944 4.28971
G>A 1791482 4.98393
G>C 1912171 5.31969
G>T 1728860 4.80972
N>C 2 5.56403e-06
N>T 2 5.56403e-06
T>A 2054037 5.71437
T>C 2204102 6.13185
T>G 2103611 5.85228
max 2mm
A>C 2930201 8.15187
A>G 2919555 8.12225
A>T 2923269 8.13258
C>A 2466008 6.86048
C>G 2540248 7.06701
C>T 2289326 6.36894
G>A 2627243 7.30904
G>C 2816437 7.83538
G>T 2586409 7.19543
N>C 4 1.11281e-05
N>G 1 2.78202e-06
N>N 1 2.78202e-06
N>T 5 1.39101e-05
T>A 3043372 8.46671
T>C 3243242 9.02276
T>G 3112334 8.65857
max 3mm
A>C 3111891 8.65733
A>G 3090860 8.59883
A>T 3102472 8.63113
C>A 2620391 7.28997
C>G 2696381 7.50138
C>T 2431542 6.76459
G>A 2781346 7.73775
G>C 2987441 8.31111
G>T 2748336 7.64592
N>A 2 5.56403e-06
N>C 5 1.39101e-05
N>G 1 2.78202e-06
N>N 1 2.78202e-06
N>T 7 1.94741e-05
T>A 3235070 9.00002
T>C 3438567 9.56615
T>G 3298886 9.17756

#q20
awk -f ../../get-mm-stats3.awk IL4-q20-m15-15mMm1kIntron.bam.md.bt
nreads 111579521
nmm 20756429
avgmm 0.186024
0 93971958
1 14763308
2 2572106
3 241850
4 28243
5 1951
6 103
7 2
A>C 1814991 8.74424
A>G 1786142 8.60525
A>T 1775415 8.55357
C>A 1562312 7.52688
C>G 1451172 6.99143
C>T 1348682 6.49766
G>A 1617433 7.79244
G>C 1604402 7.72966
G>T 1867302 8.99626
N>A 1 4.81778e-06
N>C 2 9.63557e-06
N>T 4 1.92711e-05
T>A 1827139 8.80276
T>C 2038240 9.8198
T>G 2063192 9.94001
max 1mm
A>C 1250170 6.02305
A>G 1283449 6.18338
A>T 1258222 6.06184
C>A 1118790 5.39009
C>G 1015770 4.89376
C>T 949597 4.57495
G>A 1158741 5.58256
G>C 1121243 5.40191
G>T 1374141 6.62032
N>C 2 9.63557e-06
N>T 1 4.81778e-06
T>A 1290910 6.21933
T>C 1443357 6.95378
T>G 1498915 7.22145
max 2mm
A>C 1738678 8.37658
A>G 1714992 8.26246
A>T 1699730 8.18893
C>A 1497842 7.21628
C>G 1388972 6.69177
C>T 1290217 6.21599
G>A 1553685 7.48532
G>C 1535238 7.39645
G>T 1798036 8.66255
N>C 2 9.63557e-06
N>T 3 1.44534e-05
T>A 1747139 8.41734
T>C 1957539 9.431
T>G 1985447 9.56546
max 3mm
A>C 1804083 8.69168
A>G 1775952 8.55615
A>T 1764646 8.50168
C>A 1552730 7.48072
C>G 1441806 6.94631
C>T 1340295 6.45725
G>A 1608189 7.74791
G>C 1593907 7.6791
G>T 1857444 8.94876
N>A 1 4.81778e-06
N>C 2 9.63557e-06
N>T 4 1.92711e-05
T>A 1815636 8.74734
T>C 2026522 9.76335
T>G 2051853 9.88539

#q25
awk -f ../../get-mm-stats3.awk IL4-q25-m15-15mMm1kIntron.bam.md.bt
nreads 53767451
nmm 6721440
avgmm 0.125009
0 47984394
1 4940219
2 758219
3 74500
4 9356
5 721
6 40
7 2
A>C 543507 8.08617
A>G 551485 8.20486
A>T 558897 8.31514
C>A 501412 7.45989
C>G 457980 6.81372
C>T 406797 6.05223
G>A 497390 7.40005
G>C 467143 6.95004
G>T 787603 11.7178
N>A 1 1.48778e-05
N>C 1 1.48778e-05
N>T 3 4.46333e-05
T>A 559345 8.3218
T>C 632922 9.41646
T>G 756954 11.2618
max 1mm
A>C 368142 5.47713
A>G 406036 6.04091
A>T 403702 6.00618
C>A 375493 5.5865
C>G 322998 4.80549
C>T 289733 4.31058
G>A 365540 5.43842
G>C 323743 4.81657
G>T 638808 9.50403
N>C 1 1.48778e-05
N>T 1 1.48778e-05
T>A 406871 6.05333
T>C 448134 6.66723
T>G 591017 8.79301
max 2mm
A>C 519887 7.73476
A>G 528826 7.86775
A>T 534894 7.95803
C>A 481534 7.16415
C>G 438568 6.52491
C>T 388205 5.77562
G>A 477346 7.10184
G>C 445627 6.62993
G>T 766386 11.4021
N>C 1 1.48778e-05
N>T 2 2.97555e-05
T>A 534325 7.94956
T>C 607930 9.04464
T>G 733126 10.9073
max 3mm
A>C 539771 8.03059
A>G 548063 8.15395
A>T 555270 8.26118
C>A 498271 7.41316
C>G 454846 6.76709
C>T 403920 6.00943
G>A 494261 7.3535
G>C 463671 6.89839
G>T 784278 11.6683
N>A 1 1.48778e-05
N>C 1 1.48778e-05
N>T 3 4.46333e-05
T>A 555531 8.26506
T>C 629135 9.36012
T>G 753135 11.205








awk -f /data/results/tools/formats/fastq2fasta.awk IL4-q25-m15.fastq  > IL4-q25-m15.fa
export SHRIMP_FOLDER=/data/results/tools/align/SHRiMP_2_2_3
$SHRIMP_FOLDER/bin/gmapper-cs -L /data/results/reference/mmu/mm9/mRNA-genomic-max-intron-15k/mm9-mRNA-introns1k-cs  /data/images/proton/DKlab/mr/parclip/raw/IL4-q25-m15.fa  -N 11 -n 1 --local -o 10 -v 20% -h 20% -r 30% -w 150% -e -255 -f -255  | samtools view -Sb - | samtools sort -o - - >IL4-q25-m15-15mMm1kIntron.bam 2>IL4-q25-m15-15mMm1kIntron-bam.log
#prepare flags in bam (input $i) and convert to bowtie format (output $i.md.bt):
/data/images/proton/DKlab/mr/parclip/paralyzer/README-paralyzer15.txt
for i in *-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.tr-with-1k-introns.fa  >& /dev/null > foo.bam2
    samtools view -h foo.bam2  | awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/sam2bowtie.awk2  > $i.md.bt
    mv foo.bam2 $i.md.bam
done











#@
/data/images/proton/DKlab/mr/parclip/raw/parclip-pipeline3.sh
#9 highqual start
/data/results/tools/solid/qc-filter/SOLiD_preprocess_filter_v2_MR1.pl -a on -p 9  -o 0hrep1filt7 -f 0hrep1/ugc_604_1_F3.csfasta -g 0hrep1/ugc_604_1_F3.QV.qual
cat 0hrep1filt7_T_F3.csfasta | /data/images/proton/DKlab/mr/parclip/parpipe/PARpipe-master/scripts/collapseFA.pl >  0hrep1filt7_T_F3.csfasta.coll
./SeqTrimMap4Paralyzer -m 10 -l 18 -v 2 -p 10 -i -o 0hrep1F-4p10  0hrep1filt7_T_F3.csfasta.coll  /data/results/reference/mmu/mm9/bowtie1/mm9c
/data/results/tools/samtools/samtools-1.3/misc/bowtie2sam.pl 0hrep1F-4p10.bowtie |samtools view -bS -t /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa.fai -  | samtools sort -o - - > 0hrep1F-4p10.bam;samtools index  0hrep1F-4p10.bam
/data/results/tools/align/rnaseqmut/rnaseqmut-master/bin/rnaseqmut.linux.x64 -r /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa -m 0 0hrep1F-4p10.bam  | awk -f /data/results/tools/align/rnaseqmut/count-conversions1.awk > 0hrep1F-4p10.conversion.stats
AtoC 517998 9.74356
GtoA 494720 9.3057
CtoA 393703 7.40557
TtoG 390794 7.35085
GtoC 288313 5.42318
AtoT 363640 6.84008
AtoG 408175 7.67779
GtoT 244998 4.60842
CtoT 406600 7.64816
CtoG 443212 8.33683
TtoA 669083 12.5855
TtoC 695075 13.0744

#8 highqual start
/data/results/tools/solid/qc-filter/SOLiD_preprocess_filter_v2_MR1.pl -a on -p 8  -o 0hrep1filt6 -f 0hrep1/ugc_604_1_F3.csfasta -g 0hrep1/ugc_604_1_F3.QV.qual
cat 0hrep1filt6_T_F3.csfasta | /data/images/proton/DKlab/mr/parclip/parpipe/PARpipe-master/scripts/collapseFA.pl >  0hrep1filt6_T_F3.csfasta.coll
./SeqTrimMap4Paralyzer -m 10 -l 18 -v 2 -p 10 -i -o 0hrep1F-4p9  0hrep1filt6_T_F3.csfasta.coll  /data/results/reference/mmu/mm9/bowtie1/mm9c
/data/results/tools/samtools/samtools-1.3/misc/bowtie2sam.pl 0hrep1F-4p9.bowtie |samtools view -bS -t /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa.fai -  | samtools sort -o - - > 0hrep1F-4p9.bam;samtools index !$
/data/results/tools/align/rnaseqmut/rnaseqmut-master/bin/rnaseqmut.linux.x64 -r /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa -m 0 0hrep1F-4p9.bam  | awk -f /data/results/tools/align/rnaseqmut/count-conversions1.awk > 0hrep1F-4p9.conversion.stats
AtoC 1149850 7.5904
GtoA 1240966 8.19188
TtoG 1608036 10.615
CtoA 1132298 7.47454
GtoC 1120880 7.39917
AtoT 1245940 8.22471
AtoG 1291815 8.52755
GtoT 548708 3.62214
CtoT 1344343 8.87429
CtoG 1059029 6.99088
TtoA 1893276 12.4979
TtoC 1513591 9.99154


#5 highqual start, max. 1err
/data/results/tools/solid/qc-filter/SOLiD_preprocess_filter_v2_MR1.pl -a on -p 5 -e 1  -o 0hrep1filt4 -f 0hrep1/ugc_604_1_F3.csfasta -g 0hrep1/ugc_604_1_F3.QV.qual
cat 0hrep1filt4_T_F3.csfasta | /data/images/proton/DKlab/mr/parclip/parpipe/PARpipe-master/scripts/collapseFA.pl >  0hrep1filt4_T_F3.csfasta.coll
./SeqTrimMap4Paralyzer -m 10 -l 18 -v 2 -p 10 -i -o 0hrep1F-4p7  0hrep1filt4_T_F3.csfasta.coll  /data/results/reference/mmu/mm9/bowtie1/mm9c
/data/results/tools/samtools/samtools-1.3/misc/bowtie2sam.pl 0hrep1F-4p7.bowtie |samtools view -bS -t /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa.fai -  | samtools sort -o - - > 0hrep1F-4p7.bam;samtools index !$
/data/results/tools/align/rnaseqmut/rnaseqmut-master/bin/rnaseqmut.linux.x64 -r /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa -m 0 0hrep1F-4p7.bam  | awk -f /data/results/tools/align/rnaseqmut/count-conversions1.awk > 0hrep1F-4p7.conversion.stats
AtoC 4470251 8.30193
GtoA 4059403 7.53893
TtoG 4819767 8.95104
CtoA 4181503 7.76568
GtoC 3606336 6.69751
AtoT 5108293 9.48687
AtoG 4992818 9.27242
GtoT 2463548 4.57518
CtoT 4260106 7.91166
CtoG 3603078 6.69146
TtoA 6238741 11.5863
TtoC 6042057 11.221


#10 highqual start, max. 1err
/data/results/tools/solid/qc-filter/SOLiD_preprocess_filter_v2_MR1.pl -a on -p 10 -e 1  -o 0hrep1filt3 -f 0hrep1/ugc_604_1_F3.csfasta -g 0hrep1/ugc_604_1_F3.QV.qual
cat 0hrep1filt3_T_F3.csfasta | /data/images/proton/DKlab/mr/parclip/parpipe/PARpipe-master/scripts/collapseFA.pl >  0hrep1filt3_T_F3.csfasta.coll
./SeqTrimMap4Paralyzer -m 10 -l 18 -v 2 -p 10 -i -o 0hrep1F-4p5  0hrep1filt3_T_F3.csfasta.coll  /data/results/reference/mmu/mm9/bowtie1/mm9c
/data/results/tools/samtools/samtools-1.3/misc/bowtie2sam.pl 0hrep1F-4p5.bowtie |samtools view -bS -t /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa.fai -  | samtools sort -o - - > 0hrep1F-4p5.bam;samtools index !$
/data/results/tools/align/rnaseqmut/rnaseqmut-master/bin/rnaseqmut.linux.x64 -r /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa -m 0 0hrep1F-4p5.bam  | awk -f /data/results/tools/align/rnaseqmut/count-conversions1.awk > 0hrep1F-4p5.conversion.stats
AtoC 56196 6.07166
GtoA 50695 5.47731
TtoG 109458 11.8263
CtoA 96148 10.3882
GtoC 66328 7.16636
AtoG 81383 8.79297
AtoT 78226 8.45188
GtoT 42861 4.63089
CtoG 73822 7.97605
CtoT 35355 3.81991
TtoA 109382 11.8181
TtoC 125692 13.5803

#10 highqual start, (default max. 3err)
/data/results/tools/solid/qc-filter/SOLiD_preprocess_filter_v2_MR1.pl -a on -p 10 -o 0hrep1filt2 -f 0hrep1/ugc_604_1_F3.csfasta -g 0hrep1/ugc_604_1_F3.QV.qual 
cat 0hrep1filt2_T_F3.csfasta | /data/images/proton/DKlab/mr/parclip/parpipe/PARpipe-master/scripts/collapseFA.pl >  0hrep1filt2_T_F3.csfasta.coll
./SeqTrimMap4Paralyzer -m 10 -l 18 -v 2 -p 10 -i -o 0hrep1F-4p4  0hrep1filt2_T_F3.csfasta.coll  /data/results/reference/mmu/mm9/bowtie1/mm9c
/data/results/tools/samtools/samtools-1.3/misc/bowtie2sam.pl 0hrep1F-4p4.bowtie |samtools view -bS -t /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa.fai -  | samtools sort -o - - > 0hrep1F-4p4.bam
samtools index 0hrep1F-4p4.bam
(
bam=readSortedBam("0hrep1F-4p4.bam")
countTable <- getAllSub( bam, minCov = 10 )
png("substPlot-0hrep1F-4p4.png",width=1024,height=1200,pointsize = 22)
plotSubstitutions( countTable, highlight = "TC" ) # TC 3.06% (without -p10: 2.7%)
dev.off()
)
/data/results/tools/align/rnaseqmut/rnaseqmut-master/bin/rnaseqmut.linux.x64 -r /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa -m 0 0hrep1F-4p4.bam  | awk -f /data/results/tools/align/rnaseqmut/count-conversions1.awk > 0hrep1F-4p4.conversion.stats
AtoC 79338 8.37926
GtoA 51295 5.41751
TtoG 87165 9.2059
CtoA 31930 3.37228
GtoC 68090 7.1913
AtoG 79917 8.44041
AtoT 41927 4.42811
GtoT 36403 3.84469
CtoG 69022 7.28974
CtoT 103401 10.9207
TtoA 151570 16.008
TtoC 146780 15.5021

(#1mm
./SeqTrimMap4Paralyzer -m 10 -l 18 -v 1 -p 10 -i -o 0hrep1F-4p8  0hrep1filt2_T_F3.csfasta.coll  /data/results/reference/mmu/mm9/bowtie1/mm9c
/data/results/tools/samtools/samtools-1.3/misc/bowtie2sam.pl 0hrep1F-4p8.bowtie |samtools view -bS -t /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa.fai -  | samtools sort -o - - > 0hrep1F-4p8.bam
samtools index 0hrep1F-4p8.bam
/data/results/tools/align/rnaseqmut/rnaseqmut-master/bin/rnaseqmut.linux.x64 -r /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa -m 0 0hrep1F-4p8.bam  | awk -f /data/results/tools/align/rnaseqmut/count-conversions1.awk > 0hrep1F-4p8.conversion.stats
# not mm's !
)
/data/results/tools/solid/qc-filter/SOLiD_preprocess_filter_v2_MR1.pl -p 5 -a on -o 0hrep1filt5 -f 0hrep1/ugc_604_1_F3.csfasta -g 0hrep1/ugc_604_1_F3.QV.qual

/data/results/tools/solid/qc-filter/SOLiD_preprocess_filter_v2_MR1.pl -a on -p 10 -o 0hrep1filt2 -f 0hrep1/ugc_604_1_F3.csfasta -g 0hrep1/ugc_604_1_F3.QV.qual 
# 3mm
./SeqTrimMap4Paralyzer -m 10 -l 18 -v 3 -p 10 -i -o 0hrep1F-4p6  0hrep1filt2_T_F3.csfasta.coll  /data/results/reference/mmu/mm9/bowtie1/mm9c
/data/results/tools/samtools/samtools-1.3/misc/bowtie2sam.pl 0hrep1F-4p6.bowtie |samtools view -bS -t /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa.fai -  | samtools sort -o - - > 0hrep1F-4p6.bam
samtools index !$
/data/results/tools/align/rnaseqmut/rnaseqmut-master/bin/rnaseqmut.linux.x64 -r /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa -m 0 0hrep1F-4p6.bam  | awk -f /data/results/tools/align/rnaseqmut/count-conversions1.awk > 0hrep1F-4p6.conversion.stats
AtoC 159044 11.4624
GtoA 79407 5.72293
CtoA 75531 5.44358
TtoG 91401 6.58735
GtoC 143173 10.3186
AtoT 135697 9.77979
AtoG 153727 11.0792
GtoT 49017 3.5327
CtoT 55773 4.01961
CtoG 87409 6.29964
TtoA 224802 16.2017
TtoC 132543 9.55248


# get TC stats for old TIA alignment:
reczko@max:/data/images/proton/DKlab/mr/parclip/raw$  /data/results/tools/samtools/samtools-1.3/misc/bowtie2sam.pl /data/images/proton/DKlab/mr/parclip/TIA_PARCLIPraw/csfasta/ugc_604_10_Genome.bowtie |samtools view -bS -t /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa.fai -  | samtools sort -o - - > TIA_ugc_604_10_Genome_old.bam
samtools index !$
bam=readSortedBam("TIA_ugc_604_10_Genome_old.bam"
+)
countTable <- getAllSub( bam, minCov = 10 )
png("substPlot-TIA_ugc_604_10_Genome_old.png",width=1024,height=1200,pointsize = 22)
plotSubstitutions( countTable, highlight = "TC" )
dev.off()
/data/results/tools/align/rnaseqmut/rnaseqmut-master/bin/rnaseqmut.linux.x64 -r /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa -m 0 TIA_ugc_604_10_Genome_old.bam  | awk -f /data/results/tools/align/rnaseqmut/count-conversions1.awk > TIA_ugc_604_10_Genome_old.bam.conversion.stats
AtoC 45591433 8.66212
GtoA 34800405 6.61188
CtoA 31338114 5.95407
TtoG 57667920 10.9566
GtoC 32066772 6.09251
AtoG 54808564 10.4133
AtoT 55939168 10.6281
GtoT 30513152 5.79733
CtoT 38702321 7.35323
CtoG 33019686 6.27356
TtoA 52301639 9.93702
TtoC 59581961 11.3202


/data/results/tools/align/rnaseqmut/rnaseqmut-master/bin/rnaseqmut.linux.x64 -r /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa -m 0 0hrep1F-4p3.sam.bam  | awk -f /data/results/tools/align/rnaseqmut/count-conversions1.awk > 0hrep1F-4p3.conversion.stats
AtoC 6071730 8.08974
GtoA 5410862 7.20922
TtoG 7049780 9.39285
CtoA 6334372 8.43967
GtoC 5262681 7.01179
AtoT 6778973 9.03204
AtoG 7536796 10.0417
GtoT 3268056 4.35423
CtoT 5592896 7.45176
CtoG 4956693 6.60411
TtoA 8369983 11.1518
TtoC 8421894 11.221


# SAET very likely worsens:
awk -f ../get-mm-stats3.awk /data/images/proton/DKlab/mr/parclip/raw/saet/IL4-saet-cutad-k.bowtie
nreads 24775459
nmm 8127809
avgmm 0.328059
0 17536745
1 6349619
2 889095
C>T 498077 6.12806
C>G 480398 5.91055
G>A 461061 5.67264
T>A 1070943 13.1763
A>T 657609 8.09085
G>C 537920 6.61827
A>G 764593 9.40712
T>C 803758 9.88899
C>A 454108 5.58709
G>T 596757 7.34216
T>G 742733 9.13817
A>C 1059852 13.0398
max 1mm
C>T 375706 4.62248
C>G 375067 4.61461
T>A 908247 11.1746
G>A 344951 4.24408
A>T 508665 6.25833
G>C 394870 4.85826
A>G 577092 7.10022
T>C 608136 7.48216
C>A 346528 4.26349
G>T 488132 6.0057
T>G 548267 6.74557
A>C 873958 10.7527
max 2mm
C>T 498077 6.12806
C>G 480398 5.91055
G>A 461061 5.67264
T>A 1070943 13.1763
A>T 657609 8.09085
G>C 537920 6.61827
A>G 764593 9.40712
T>C 803758 9.88899
C>A 454108 5.58709
G>T 596757 7.34216
T>G 742733 9.13817
A>C 1059852 13.0398
max 3mm
C>T 498077 6.12806
C>G 480398 5.91055
G>A 461061 5.67264
T>A 1070943 13.1763
A>T 657609 8.09085
G>C 537920 6.61827
A>G 764593 9.40712
T>C 803758 9.88899
C>A 454108 5.58709
G>T 596757 7.34216
T>G 742733 9.13817
A>C 1059852 13.0398


#@ genomic alignments:
reczko@max:/data/images/proton/DKlab/mr/parclip/genome$ awk -f ../get-mm-stats3.awk IL4-q25.bam.md.bt 
nreads 53767526
nmm 7607889
avgmm 0.141496
0 47214565
1 5607598
2 846502
3 88827
4 9385
5 629
6 19
7 1
C>G 522138 6.86311
C>T 450596 5.92275
G>A 449522 5.90863
T>A 729203 9.58483
N>T 1 1.31443e-05
A>T 816416 10.7312
G>C 496280 6.52323
T>C 746788 9.81597
A>G 1016025 13.3549
G>T 458408 6.02543
C>A 531674 6.98846
T>G 751860 9.88264
N>A 1 1.31443e-05
A>C 638977 8.39887
max 1mm
C>G 383665 5.04299
C>T 325513 4.27862
G>A 327104 4.29954
T>A 524494 6.89408
A>T 621228 8.16558
G>C 328784 4.32162
T>C 552907 7.26755
A>G 791578 10.4047
G>T 331930 4.36297
C>A 404757 5.32023
T>G 560873 7.37226
A>C 454765 5.97755
max 2mm
C>G 500598 6.57999
C>T 431943 5.67757
G>A 430690 5.6611
T>A 697390 9.16667
A>T 786525 10.3383
G>C 471533 6.19795
T>C 714872 9.39646
A>G 982897 12.9194
G>T 438785 5.7675
C>A 512702 6.73908
T>G 723049 9.50394
A>C 609618 8.01297
max 3mm
C>G 519283 6.82559
C>T 448097 5.8899
G>A 446998 5.87545
T>A 725281 9.53328
N>T 1 1.31443e-05
A>T 812506 10.6798
G>C 493017 6.48034
T>C 742404 9.75834
A>G 1011362 13.2936
G>T 455780 5.99089
C>A 529158 6.95539
T>G 748069 9.83281
N>A 1 1.31443e-05
A>C 635126 8.34826