######  running STAR for sample_1, replicate_1#####
STAR --chimSegmentMin 2 --outFilterMismatchNmax 3 --alignEndsType EndToEnd --runThreadN 4 --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate --alignSJDBoverhangMin 6 --alignIntronMax 300000 --genomeDir /cbcl/forouzme/Projects/PolyA/rMATS/mm9-star/ --sjdbGTFfile gtf/Mus_musculus.Ensembl.NCBIM37.65.gtf --outFileNamePrefix /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/SAMPLE_1/REP_1/ --readFilesIn /cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/Wt1-hind1-paired.fastq /cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/Wt1-hind2-paired.fastq
#
######  running STAR for sample_1, replicate_2#####
STAR --chimSegmentMin 2 --outFilterMismatchNmax 3 --alignEndsType EndToEnd --runThreadN 4 --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate --alignSJDBoverhangMin 6 --alignIntronMax 300000 --genomeDir /cbcl/forouzme/Projects/PolyA/rMATS/mm9-star/ --sjdbGTFfile gtf/Mus_musculus.Ensembl.NCBIM37.65.gtf --outFileNamePrefix /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/SAMPLE_1/REP_2/ --readFilesIn /cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/Wt2-hind1-paired.fastq /cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/Wt2-hind2-paired.fastq
#
######  running STAR for sample_1, replicate_3#####
STAR --chimSegmentMin 2 --outFilterMismatchNmax 3 --alignEndsType EndToEnd --runThreadN 4 --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate --alignSJDBoverhangMin 6 --alignIntronMax 300000 --genomeDir /cbcl/forouzme/Projects/PolyA/rMATS/mm9-star/ --sjdbGTFfile gtf/Mus_musculus.Ensembl.NCBIM37.65.gtf --outFileNamePrefix /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/SAMPLE_1/REP_3/ --readFilesIn /cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/Wt3-hind1-paired.fastq /cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/Wt3-hind2-paired.fastq
#
######  running STAR for sample_1, replicate_4#####
STAR --chimSegmentMin 2 --outFilterMismatchNmax 3 --alignEndsType EndToEnd --runThreadN 4 --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate --alignSJDBoverhangMin 6 --alignIntronMax 300000 --genomeDir /cbcl/forouzme/Projects/PolyA/rMATS/mm9-star/ --sjdbGTFfile gtf/Mus_musculus.Ensembl.NCBIM37.65.gtf --outFileNamePrefix /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/SAMPLE_1/REP_4/ --readFilesIn /cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/Wt4-hind1-paired.fastq /cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/Wt4-hind2-paired.fastq
#
######  running STAR for sample_2, replicate_1#####
STAR --chimSegmentMin 2 --outFilterMismatchNmax 3 --alignEndsType EndToEnd --runThreadN 4 --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate --alignSJDBoverhangMin 6 --alignIntronMax 300000 --genomeDir /cbcl/forouzme/Projects/PolyA/rMATS/mm9-star/ --sjdbGTFfile gtf/Mus_musculus.Ensembl.NCBIM37.65.gtf --outFileNamePrefix /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/SAMPLE_2/REP_1/ --readFilesIn /cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/KO1-hind1-paired.fastq /cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/KO1-hind2-paired.fastq
#
######  running STAR for sample_2, replicate_2#####
STAR --chimSegmentMin 2 --outFilterMismatchNmax 3 --alignEndsType EndToEnd --runThreadN 4 --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate --alignSJDBoverhangMin 6 --alignIntronMax 300000 --genomeDir /cbcl/forouzme/Projects/PolyA/rMATS/mm9-star/ --sjdbGTFfile gtf/Mus_musculus.Ensembl.NCBIM37.65.gtf --outFileNamePrefix /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/SAMPLE_2/REP_2/ --readFilesIn /cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/KO2-hind1-paired.fastq /cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/KO2-hind2-paired.fastq
#
######  running STAR for sample_2, replicate_3#####
STAR --chimSegmentMin 2 --outFilterMismatchNmax 3 --alignEndsType EndToEnd --runThreadN 4 --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate --alignSJDBoverhangMin 6 --alignIntronMax 300000 --genomeDir /cbcl/forouzme/Projects/PolyA/rMATS/mm9-star/ --sjdbGTFfile gtf/Mus_musculus.Ensembl.NCBIM37.65.gtf --outFileNamePrefix /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/SAMPLE_2/REP_3/ --readFilesIn /cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/KO3-hind1-paired.fastq /cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/KO3-hind2-paired.fastq
#
######  running STAR for sample_2, replicate_4#####
STAR --chimSegmentMin 2 --outFilterMismatchNmax 3 --alignEndsType EndToEnd --runThreadN 4 --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate --alignSJDBoverhangMin 6 --alignIntronMax 300000 --genomeDir /cbcl/forouzme/Projects/PolyA/rMATS/mm9-star/ --sjdbGTFfile gtf/Mus_musculus.Ensembl.NCBIM37.65.gtf --outFileNamePrefix /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/SAMPLE_2/REP_4/ --readFilesIn /cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/KO4-hind1-paired.fastq /cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/KO4-hind2-paired.fastq
#
###### getting AS events from GTF and BAM files #####
python /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/bin/processGTF.BAMs.py gtf/Mus_musculus.Ensembl.NCBIM37.65.gtf /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/ASEvents/fromGTF /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/SAMPLE_1/REP_1/aligned.sorted.bam,/dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/SAMPLE_1/REP_2/aligned.sorted.bam,/dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/SAMPLE_1/REP_3/aligned.sorted.bam,/dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/SAMPLE_1/REP_4/aligned.sorted.bam,/dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/SAMPLE_2/REP_1/aligned.sorted.bam,/dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/SAMPLE_2/REP_2/aligned.sorted.bam,/dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/SAMPLE_2/REP_3/aligned.sorted.bam,/dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/SAMPLE_2/REP_4/aligned.sorted.bam fr-unstranded PE 1 /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp
#
###### making MATS input from AS events and BAM files #####
python /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/bin/MATS.processsUnique.bam.py /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/config.txt
#
###### running MATS input for SE using Junction Counts only #####
awk '{ split($2,ic_1,","); sum_ic_1=0; for (x in ic_1) sum_ic_1 += ic_1[x]; split($4,ic_2,","); sum_ic_2=0; for (x in ic_2) sum_ic_2 += ic_2[x]; split($3,sc_1,","); sum_sc_1=0; for (x in sc_1) sum_sc_1 += sc_1[x]; split($5,sc_2,","); sum_sc_2=0; for (x in sc_2) sum_sc_2 += sc_2[x]; if ( NR==1 || ( (sum_ic_2 + sum_sc_2 > 0) && (sum_ic_1 + sum_sc_1 > 0) && (sum_ic_1 != 0 || sum_ic_2 != 0) && (sum_sc_1 != 0 || sum_sc_2 != 0) && $6!=0 && $7!=0 ) ) {print $0}}' /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/JC.RNASeq.SE.MATS.input.txt > /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/SE.JC.input.txt;/dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/MATS/rMATS.sh -d /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/SE.JC.input.txt -o /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/SEout_JC/ -c 0.0001 -p 4 -t U
#
###### running MATS input for SE using Junction Counts and Reads on target Exon Counts #####
awk '{ split($2,ic_1,","); sum_ic_1=0; for (x in ic_1) sum_ic_1 += ic_1[x]; split($4,ic_2,","); sum_ic_2=0; for (x in ic_2) sum_ic_2 += ic_2[x]; split($3,sc_1,","); sum_sc_1=0; for (x in sc_1) sum_sc_1 += sc_1[x]; split($5,sc_2,","); sum_sc_2=0; for (x in sc_2) sum_sc_2 += sc_2[x]; if ( NR==1 || ( (sum_ic_2 + sum_sc_2 > 0) && (sum_ic_1 + sum_sc_1 > 0) && (sum_ic_1 != 0 || sum_ic_2 != 0) && (sum_sc_1 != 0 || sum_sc_2 != 0) && $6!=0 && $7!=0 ) ) {print $0}}' /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/JCEC.RNASeq.SE.MATS.input.txt > /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/SE.JCEC.input.txt;/dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/MATS/rMATS.sh -d /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/SE.JCEC.input.txt -o /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/SEout_JCEC/ -c 0.0001 -p 8 -t U
#
###### running MATS input for MXE using Junction Counts only #####
awk '{ split($2,ic_1,","); sum_ic_1=0; for (x in ic_1) sum_ic_1 += ic_1[x]; split($4,ic_2,","); sum_ic_2=0; for (x in ic_2) sum_ic_2 += ic_2[x]; split($3,sc_1,","); sum_sc_1=0; for (x in sc_1) sum_sc_1 += sc_1[x]; split($5,sc_2,","); sum_sc_2=0; for (x in sc_2) sum_sc_2 += sc_2[x]; if ( NR==1 || ( (sum_ic_2 + sum_sc_2 > 0) && (sum_ic_1 + sum_sc_1 > 0) && (sum_ic_1 != 0 || sum_ic_2 != 0) && (sum_sc_1 != 0 || sum_sc_2 != 0) && $6!=0 && $7!=0 ) ) {print $0}}' /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/JC.RNASeq.MXE.MATS.input.txt > /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/MXE.JC.input.txt;/dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/MATS/rMATS.sh -d /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/MXE.JC.input.txt -o /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/MXEout_JC/ -c 0.0001 -p 4 -t U
#
###### running MATS input for MXE using Junction Counts and Reads on target Exon Counts #####
awk '{ split($2,ic_1,","); sum_ic_1=0; for (x in ic_1) sum_ic_1 += ic_1[x]; split($4,ic_2,","); sum_ic_2=0; for (x in ic_2) sum_ic_2 += ic_2[x]; split($3,sc_1,","); sum_sc_1=0; for (x in sc_1) sum_sc_1 += sc_1[x]; split($5,sc_2,","); sum_sc_2=0; for (x in sc_2) sum_sc_2 += sc_2[x]; if ( NR==1 || ( (sum_ic_2 + sum_sc_2 > 0) && (sum_ic_1 + sum_sc_1 > 0) && (sum_ic_1 != 0 || sum_ic_2 != 0) && (sum_sc_1 != 0 || sum_sc_2 != 0) && $6!=0 && $7!=0 ) ) {print $0}}' /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/JCEC.RNASeq.MXE.MATS.input.txt > /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/MXE.JCEC.input.txt;/dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/MATS/rMATS.sh -d /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/MXE.JCEC.input.txt -o /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/MXEout_JCEC/ -c 0.0001 -p 8 -t U
#
###### running MATS input for A5SS using Junction Counts only #####
awk '{ split($2,ic_1,","); sum_ic_1=0; for (x in ic_1) sum_ic_1 += ic_1[x]; split($4,ic_2,","); sum_ic_2=0; for (x in ic_2) sum_ic_2 += ic_2[x]; split($3,sc_1,","); sum_sc_1=0; for (x in sc_1) sum_sc_1 += sc_1[x]; split($5,sc_2,","); sum_sc_2=0; for (x in sc_2) sum_sc_2 += sc_2[x]; if ( NR==1 || ( (sum_ic_2 + sum_sc_2 > 0) && (sum_ic_1 + sum_sc_1 > 0) && (sum_ic_1 != 0 || sum_ic_2 != 0) && (sum_sc_1 != 0 || sum_sc_2 != 0) && $6!=0 && $7!=0 ) ) {print $0}}' /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/JC.RNASeq.A5SS.MATS.input.txt > /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/A5SS.JC.input.txt;/dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/MATS/rMATS.sh -d /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/A5SS.JC.input.txt -o /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/A5SSout_JC/ -c 0.0001 -p 4 -t U
#
###### running MATS input for A5SS using Junction Counts and Reads on target Exon Counts #####
awk '{ split($2,ic_1,","); sum_ic_1=0; for (x in ic_1) sum_ic_1 += ic_1[x]; split($4,ic_2,","); sum_ic_2=0; for (x in ic_2) sum_ic_2 += ic_2[x]; split($3,sc_1,","); sum_sc_1=0; for (x in sc_1) sum_sc_1 += sc_1[x]; split($5,sc_2,","); sum_sc_2=0; for (x in sc_2) sum_sc_2 += sc_2[x]; if ( NR==1 || ( (sum_ic_2 + sum_sc_2 > 0) && (sum_ic_1 + sum_sc_1 > 0) && (sum_ic_1 != 0 || sum_ic_2 != 0) && (sum_sc_1 != 0 || sum_sc_2 != 0) && $6!=0 && $7!=0 ) ) {print $0}}' /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/JCEC.RNASeq.A5SS.MATS.input.txt > /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/A5SS.JCEC.input.txt;/dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/MATS/rMATS.sh -d /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/A5SS.JCEC.input.txt -o /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/A5SSout_JCEC/ -c 0.0001 -p 8 -t U
#
###### running MATS input for A3SS using Junction Counts only #####
awk '{ split($2,ic_1,","); sum_ic_1=0; for (x in ic_1) sum_ic_1 += ic_1[x]; split($4,ic_2,","); sum_ic_2=0; for (x in ic_2) sum_ic_2 += ic_2[x]; split($3,sc_1,","); sum_sc_1=0; for (x in sc_1) sum_sc_1 += sc_1[x]; split($5,sc_2,","); sum_sc_2=0; for (x in sc_2) sum_sc_2 += sc_2[x]; if ( NR==1 || ( (sum_ic_2 + sum_sc_2 > 0) && (sum_ic_1 + sum_sc_1 > 0) && (sum_ic_1 != 0 || sum_ic_2 != 0) && (sum_sc_1 != 0 || sum_sc_2 != 0) && $6!=0 && $7!=0 ) ) {print $0}}' /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/JC.RNASeq.A3SS.MATS.input.txt > /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/A3SS.JC.input.txt;/dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/MATS/rMATS.sh -d /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/A3SS.JC.input.txt -o /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/A3SSout_JC/ -c 0.0001 -p 4 -t U
#
###### running MATS input for A3SS using Junction Counts and Reads on target Exon Counts #####
awk '{ split($2,ic_1,","); sum_ic_1=0; for (x in ic_1) sum_ic_1 += ic_1[x]; split($4,ic_2,","); sum_ic_2=0; for (x in ic_2) sum_ic_2 += ic_2[x]; split($3,sc_1,","); sum_sc_1=0; for (x in sc_1) sum_sc_1 += sc_1[x]; split($5,sc_2,","); sum_sc_2=0; for (x in sc_2) sum_sc_2 += sc_2[x]; if ( NR==1 || ( (sum_ic_2 + sum_sc_2 > 0) && (sum_ic_1 + sum_sc_1 > 0) && (sum_ic_1 != 0 || sum_ic_2 != 0) && (sum_sc_1 != 0 || sum_sc_2 != 0) && $6!=0 && $7!=0 ) ) {print $0}}' /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/JCEC.RNASeq.A3SS.MATS.input.txt > /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/A3SS.JCEC.input.txt;/dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/MATS/rMATS.sh -d /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/A3SS.JCEC.input.txt -o /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/A3SSout_JCEC/ -c 0.0001 -p 8 -t U
#
###### running MATS input for RI using Junction Counts only #####
awk '{ split($2,ic_1,","); sum_ic_1=0; for (x in ic_1) sum_ic_1 += ic_1[x]; split($4,ic_2,","); sum_ic_2=0; for (x in ic_2) sum_ic_2 += ic_2[x]; split($3,sc_1,","); sum_sc_1=0; for (x in sc_1) sum_sc_1 += sc_1[x]; split($5,sc_2,","); sum_sc_2=0; for (x in sc_2) sum_sc_2 += sc_2[x]; if ( NR==1 || ( (sum_ic_2 + sum_sc_2 > 0) && (sum_ic_1 + sum_sc_1 > 0) && (sum_ic_1 != 0 || sum_ic_2 != 0) && (sum_sc_1 != 0 || sum_sc_2 != 0) && $6!=0 && $7!=0 ) ) {print $0}}' /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/JC.RNASeq.RI.MATS.input.txt > /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/RI.JC.input.txt;/dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/MATS/rMATS.sh -d /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/RI.JC.input.txt -o /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/RIout_JC/ -c 0.0001 -p 4 -t U
#
###### running MATS input for RI using Junction Counts and Reads on target Exon Counts #####
awk '{ split($2,ic_1,","); sum_ic_1=0; for (x in ic_1) sum_ic_1 += ic_1[x]; split($4,ic_2,","); sum_ic_2=0; for (x in ic_2) sum_ic_2 += ic_2[x]; split($3,sc_1,","); sum_sc_1=0; for (x in sc_1) sum_sc_1 += sc_1[x]; split($5,sc_2,","); sum_sc_2=0; for (x in sc_2) sum_sc_2 += sc_2[x]; if ( NR==1 || ( (sum_ic_2 + sum_sc_2 > 0) && (sum_ic_1 + sum_sc_1 > 0) && (sum_ic_1 != 0 || sum_ic_2 != 0) && (sum_sc_1 != 0 || sum_sc_2 != 0) && $6!=0 && $7!=0 ) ) {print $0}}' /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/JCEC.RNASeq.RI.MATS.input.txt > /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/RI.JCEC.input.txt;/dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/MATS/rMATS.sh -d /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/RI.JCEC.input.txt -o /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/RIout_JCEC/ -c 0.0001 -p 8 -t U
#
###### joining MATS results for SE using Junction Counts only #####
python /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/bin/joinFiles.py /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/ASEvents/fromGTF.SE.txt /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/SEout_JC/rMATS_Result.txt  0 0 /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/SE.MATS.JunctionCountOnly.txt ; awk '{print $(NF-3),$0}' /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/SE.MATS.JunctionCountOnly.txt | sort -g | cut -d' ' -f2- > /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/MATS_output/SE.MATS.JunctionCountOnly.txt
#
###### joining MATS results for SE using Junction Counts and Reads on target Exon Counts #####
python /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/bin/joinFiles.py /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/ASEvents/fromGTF.SE.txt /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/SEout_JCEC/rMATS_Result.txt  0 0 /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/SE.MATS.JunctionCountOnly.txt ; awk '{print $(NF-3),$0}' /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/SE.MATS.JunctionCountOnly.txt | sort -g | cut -d' ' -f2- > /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/MATS_output/SE.MATS.ReadsOnTargetAndJunctionCounts.txt
#
###### joining MATS results for MXE using Junction Counts only #####
python /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/bin/joinFiles.py /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/ASEvents/fromGTF.MXE.txt /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/MXEout_JC/rMATS_Result.txt  0 0 /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/MXE.MATS.JunctionCountOnly.txt ; awk '{print $(NF-3),$0}' /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/MXE.MATS.JunctionCountOnly.txt | sort -g | cut -d' ' -f2- > /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/MATS_output/MXE.MATS.JunctionCountOnly.txt
#
###### joining MATS results for MXE using Junction Counts and Reads on target Exon Counts #####
python /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/bin/joinFiles.py /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/ASEvents/fromGTF.MXE.txt /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/MXEout_JCEC/rMATS_Result.txt  0 0 /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/MXE.MATS.JunctionCountOnly.txt ; awk '{print $(NF-3),$0}' /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/MXE.MATS.JunctionCountOnly.txt | sort -g | cut -d' ' -f2- > /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/MATS_output/MXE.MATS.ReadsOnTargetAndJunctionCounts.txt
#
###### joining MATS results for A5SS using Junction Counts only #####
python /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/bin/joinFiles.py /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/ASEvents/fromGTF.A5SS.txt /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/A5SSout_JC/rMATS_Result.txt  0 0 /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/A5SS.MATS.JunctionCountOnly.txt ; awk '{print $(NF-3),$0}' /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/A5SS.MATS.JunctionCountOnly.txt | sort -g | cut -d' ' -f2- > /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/MATS_output/A5SS.MATS.JunctionCountOnly.txt
#
###### joining MATS results for A5SS using Junction Counts and Reads on target Exon Counts #####
python /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/bin/joinFiles.py /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/ASEvents/fromGTF.A5SS.txt /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/A5SSout_JCEC/rMATS_Result.txt  0 0 /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/A5SS.MATS.JunctionCountOnly.txt ; awk '{print $(NF-3),$0}' /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/A5SS.MATS.JunctionCountOnly.txt | sort -g | cut -d' ' -f2- > /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/MATS_output/A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt
#
###### joining MATS results for A3SS using Junction Counts only #####
python /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/bin/joinFiles.py /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/ASEvents/fromGTF.A3SS.txt /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/A3SSout_JC/rMATS_Result.txt  0 0 /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/A3SS.MATS.JunctionCountOnly.txt ; awk '{print $(NF-3),$0}' /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/A3SS.MATS.JunctionCountOnly.txt | sort -g | cut -d' ' -f2- > /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/MATS_output/A3SS.MATS.JunctionCountOnly.txt
#
###### joining MATS results for A3SS using Junction Counts and Reads on target Exon Counts #####
python /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/bin/joinFiles.py /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/ASEvents/fromGTF.A3SS.txt /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/A3SSout_JCEC/rMATS_Result.txt  0 0 /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/A3SS.MATS.JunctionCountOnly.txt ; awk '{print $(NF-3),$0}' /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/A3SS.MATS.JunctionCountOnly.txt | sort -g | cut -d' ' -f2- > /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/MATS_output/A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt
#
###### joining MATS results for RI using Junction Counts only #####
python /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/bin/joinFiles.py /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/ASEvents/fromGTF.RI.txt /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/RIout_JC/rMATS_Result.txt  0 0 /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/RI.MATS.JunctionCountOnly.txt ; awk '{print $(NF-3),$0}' /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/RI.MATS.JunctionCountOnly.txt | sort -g | cut -d' ' -f2- > /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/MATS_output/RI.MATS.JunctionCountOnly.txt
#
###### joining MATS results for RI using Junction Counts and Reads on target Exon Counts #####
python /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/bin/joinFiles.py /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/ASEvents/fromGTF.RI.txt /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/RIout_JCEC/rMATS_Result.txt  0 0 /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/RI.MATS.JunctionCountOnly.txt ; awk '{print $(NF-3),$0}' /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/temp/RI.MATS.JunctionCountOnly.txt | sort -g | cut -d' ' -f2- > /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9/MATS_output/RI.MATS.ReadsOnTargetAndJunctionCounts.txt
#