#build colorspace index
reczko@fix:/data/results/reference/mmu/mm9/bowtie1$ /data/results/tools/align/bowtie-1.2.1.1/bowtie-build -C ../../Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa mm9c

# get seqs
# ids in ~/bak/doc/fleming/kafasla/sample-ids.txt
reczko@max:/data/images/proton/DKlab/mr/parclip/raw$ tar xzvf /mnt/max/c/hazapis/Backups/ugc_604_1.tar.gz
tar xzvf /mnt/max/c/hazapis/Backups/ugc_604_4.tar.gz
tar xzvf /mnt/max/c/hazapis/Backups/ugc_604_7.tar.gz 
tar xzvf /mnt/max/c/hazapis/Backups/ugc_604_2.tar.gz
tar xzvf /mnt/max/c/hazapis/Backups/ugc_604_5.tar.gz
tar xzvf /mnt/max/c/hazapis/Backups/ugc_604_8.tar.gz
tar xzvf /mnt/max/c/hazapis/Backups/ugc_604_3.tar.gz
tar xzvf /mnt/max/c/hazapis/Backups/ugc_604_6.tar.gz
tar xzvf /mnt/max/c/hazapis/Backups/ugc_604_9.tar.gz
tar xzvf /mnt/max/c/hazapis/Backups/ugc_604_10.tar.gz
tar xzvf /mnt/max/c/hazapis/Backups/ugc_604_11.tar.gz 
ln -s ugc_604_1 0hrep1
ln -s ugc_604_4 0hrep2
ln -s ugc_604_7 0hrep3

(# adapter removal
time /data/results/tools/adapter/cutadapt-1.9.1/bin/cutadapt -q 20 -z -m 20 -c -a CGCCTTGGCCGTACAGCAG 0hrep1/ugc_604_1_F3.csfasta  0hrep1/ugc_604_1_F3.QV.qual >& 0hrep1.log > 0hrep1.fastq
/data/results/tools/adapter/cutadapt-1.9.1/bin/cutadapt -q 20 -z -m 20 -c -a CGCCTTGGCCGTACAGCAG 0hrep2/ugc_604_4_F3.csfasta  0hrep2/ugc_604_4_F3.QV.qual >& 0hrep2.log > 0hrep2.fastq
/data/results/tools/adapter/cutadapt-1.9.1/bin/cutadapt -q 20 -z -m 20 -c -a CGCCTTGGCCGTACAGCAG 0hrep3/ugc_604_7_F3.csfasta  0hrep3/ugc_604_7_F3.QV.qual >& 0hrep3.log > 0hrep3.fastq
)

#quality filtering
/data/results/tools/solid/qc-filter/SOLiD_preprocess_filter_v2.pl -a on -o 0hrep1filt -f 0hrep1/ugc_604_1_F3.csfasta -g 0hrep1/ugc_604_1_F3.QV.qual 
341609082 Sep 26 20:30 0hrep1filt_T_F3.csfasta
Count of reads in QV Analysis - Fragment Total: 11483855
Count of reads in QV Analysis - Fragment Passed: 4917630 

#errors (encoded by ".") are counted only in the first 20 colors
/data/results/tools/solid/qc-filter/SOLiD_preprocess_filter_v2_MR1.pl -a on -o 0hrep1filt2 -f 0hrep1/ugc_604_1_F3.csfasta -g 0hrep1/ugc_604_1_F3.QV.qual 
782366844 Sep 26 20:48 0hrep1filt2_T_F3.csfasta
Count of reads in QV Analysis - Fragment Passed: 11246516 
  

# alignment
(reczko@max:/data/images/proton/DKlab/mr/parclip/raw$ /data/results/tools/align/bowtie-0.12.9/bowtie /data/results/reference/mmu/mm9/bowtie1/mm9c -C -v 2 -m 10 --best --strata -q 0hrep1.fastq  > 0hrep1.bowtie
5_633_1580_F3	-	chr1	28104248	ATTGAAGATCACCATTATG	T]\LN\VLR__4&Q__[JN	4	7:T>C
grep 5_633_1580_F3 /data/results/fleming/hazapis/HuR_CLIPs_Sweden/mRNAnew/genome/0hrep1/0hrepl1.bowtie
5_633_1580_F3	-	chr1	28104244	AGAAATTGAAGATCAACATTATGG	Iq!!qqqqqqqqqq!!qqqqqqqI	0	8:T>A
/data/results/tools/align/bowtie-0.12.9/bowtie /data/results/reference/mmu/mm9/bowtie1/mm9c -C -v 2 -m 10 --best --strata -q 0hrep2.fastq  > 0hrep2.bowtie
/data/results/tools/align/bowtie-0.12.9/bowtie /data/results/reference/mmu/mm9/bowtie1/mm9c -C -v 2 -m 10 --best --strata -q 0hrep3.fastq  > 0hrep3.bowtie



/data/results/tools/align/bowtie-0.12.9/bowtie /data/results/reference/mmu/mm9/bowtie1/mm9c -C -v 2 -m 10 --best --strata -f IGGfilt2_T_F3.csfasta.coll > IGGfilt2_T_F3.csfasta.coll.bowtie
/data/results/tools/align/bowtie-0.12.9/bowtie /data/results/reference/mmu/mm9/bowtie1/mm9c -C -v 2 -m 10 --best --strata -S -f IGGfilt2_T_F3.csfasta.coll --quiet | samtools view -hS -F 4 - > IGGfilt2_T_F3.csfasta.coll.sam

)

reczko@max:/data/images/proton/DKlab/mr/parclip/raw$ ./SeqTrimMap  -m 10 -k -p 10 -i -o 0h 0hrep1/ugc_604_1_F3.csfasta  /data/results/reference/mmu/mm9/bowtie1/mm9c
reczko@max:/data/images/proton/DKlab/mr/parclip/raw$ ./SeqTrimMap2  -m 10 -k -p 10 -i -o 0hrep2 0hrep2/ugc_604_4_F3.csfasta  /data/results/reference/mmu/mm9/bowtie1/mm9c
./SeqTrimMap  -m 10 -k -p 10 -i -o IGG IGG/ugc_604_12_F3.csfasta  /data/results/reference/mmu/mm9/bowtie1/mm9c

#default settings
reczko@max:/data/images/proton/DKlab/mr/parclip/raw$ ./SeqTrimMap2  -p 8 -i -o 0hrep1b 0hrep1/ugc_604_1_F3.csfasta  /data/results/reference/mmu/mm9/bowtie1/mm9c


reczko@max:/data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_5$ ./PARalyzer 90G sample.ini-0h-b
I identified a total of 17174449 reads mapping to 3321075 Unique genomic coordinates
Making up 193924 groups
Consisting of 75266 clusters

-rw-r--r-- 1 reczko users  13470018 Sep 24 21:57 groups0h.txt
-rw-r--r-- 1 reczko users 255502219 Sep 24 21:57 distributions0h.txt
-rw-r--r-- 1 reczko users   6274075 Sep 24 21:57 clusters0h.txt
-rw-r--r-- 1 reczko users      6109 Sep 24 16:55 sample.ini-0h-b
# ~5h runtime

/data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_5/README.txt
#Paralyzer
#Recommended BOWTIE parameters:
#>bowtie GENOME_INDEX -v 2 -m 10 --best --strata -f INPUT_FASTA_FILE OUTPUT_FILE