0h :Found 30043 exon skipping events 2h :Found 29318 exon skipping events 6h :Found 29167 exon skipping events IFN:Found 28833 exon skipping events IL4:Found 27641 exon skipping events 0h :Found 3581 exon MX events 2h :Found 3655 exon MX events 6h :Found 3685 exon MX events IFN:Found 3589 exon MX events IL4:Found 3029 exon MX events 0h :There are 3827 alt 3 SS events and 2238 alt 5 SS events. 2h :There are 3802 alt 3 SS events and 2207 alt 5 SS events. 6h :There are 3772 alt 3 SS events and 2183 alt 5 SS events. IFN:There are 3768 alt 3 SS events and 2189 alt 5 SS events. IL4:There are 3770 alt 3 SS events and 2200 alt 5 SS events. 0h :Found 3207 RI events 2h :Found 3183 RI events 6h :Found 3181 RI events IFN:Found 3189 RI events IL4:Found 3187 RI events python /data/results/tools/rnaseq/mats/rMATS.4.0.2/rMATS-turbo-Linux-UCS4/rmats.py --b1 ~/bak/doc/fleming/kafasla/DKlab/mr/tzanos/rnaseq/rmats/wt0h.txt --b2 ~/bak/doc/fleming/kafasla/DKlab/mr/tzanos/rnaseq/rmats/ko0h.txt --gtf /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf --od rmats-0h -t paired --nthread 16 --readLength 100 --anchorLength 1 --tstat 16 There are 37310 distinct gene ID in the gtf file There are 95495 distinct transcript ID in the gtf file There are 22375 one-transcript genes in the gtf file There are 677632 exons in the gtf file There are 13138 one-exon transcripts in the gtf file There are 12021 one-transcript genes with only one exon in the transcript Average number of transcripts per gene is 2.559501 Average number of exons per transcript is 7.095995 Average number of exons per transcript excluding one-exon tx is 8.068458 Average number of gene per geneGroup is 6.327349 ========== Done processing each gene from dictionary to compile AS events Found 30043 exon skipping events Found 3581 exon MX events Found 6065 alt SS events There are 3827 alt 3 SS events and 2238 alt 5 SS events. Found 3207 RI events ========== Running the statistical part. The statistical part is done. Done. for i in rmats-0h/*.JC.txt do echo $i awk -f count-sig.awk $i done rmats-0h/A3SS.MATS.JC.txt 74 rmats-0h/A5SS.MATS.JC.txt 59 rmats-0h/MXE.MATS.JC.txt rmats-0h/RI.MATS.JC.txt 90 rmats-0h/SE.MATS.JC.txt 745 python /data/results/tools/rnaseq/mats/rMATS.4.0.2/rMATS-turbo-Linux-UCS4/rmats.py --b1 ~/bak/doc/fleming/kafasla/DKlab/mr/tzanos/rnaseq/rmats/wt2h.txt --b2 ~/bak/doc/fleming/kafasla/DKlab/mr/tzanos/rnaseq/rmats/ko2h.txt --gtf /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf --od rmats-2h -t paired --nthread 16 --readLength 100 --anchorLength 1 --tstat 16 There are 37310 distinct gene ID in the gtf file There are 95495 distinct transcript ID in the gtf file There are 22375 one-transcript genes in the gtf file There are 677632 exons in the gtf file There are 13138 one-exon transcripts in the gtf file There are 12021 one-transcript genes with only one exon in the transcript Average number of transcripts per gene is 2.559501 Average number of exons per transcript is 7.095995 Average number of exons per transcript excluding one-exon tx is 8.068458 Average number of gene per geneGroup is 6.327349 ========== Done processing each gene from dictionary to compile AS events Found 29318 exon skipping events Found 3655 exon MX events Found 6009 alt SS events There are 3802 alt 3 SS events and 2207 alt 5 SS events. Found 3183 RI events ========== Running the statistical part. The statistical part is done. Done. for i in rmats-2h/*.JC.txt do echo $i awk -f count-sig.awk $i done > > > > rmats-2h/A3SS.MATS.JC.txt 60 rmats-2h/A5SS.MATS.JC.txt 52 rmats-2h/MXE.MATS.JC.txt rmats-2h/RI.MATS.JC.txt 56 rmats-2h/SE.MATS.JC.txt 635 python /data/results/tools/rnaseq/mats/rMATS.4.0.2/rMATS-turbo-Linux-UCS4/rmats.py --b1 ~/bak/doc/fleming/kafasla/DKlab/mr/tzanos/rnaseq/rmats/wt6h.txt --b2 ~/bak/doc/fleming/kafasla/DKlab/mr/tzanos/rnaseq/rmats/ko6h.txt --gtf /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf --od rmats-6h -t paired --nthread 16 --readLength 100 --anchorLength 1 --tstat 16 There are 37310 distinct gene ID in the gtf file There are 95495 distinct transcript ID in the gtf file There are 22375 one-transcript genes in the gtf file There are 677632 exons in the gtf file There are 13138 one-exon transcripts in the gtf file There are 12021 one-transcript genes with only one exon in the transcript Average number of transcripts per gene is 2.559501 Average number of exons per transcript is 7.095995 Average number of exons per transcript excluding one-exon tx is 8.068458 Average number of gene per geneGroup is 6.327349 ========== Done processing each gene from dictionary to compile AS events Found 29167 exon skipping events Found 3685 exon MX events Found 5955 alt SS events There are 3772 alt 3 SS events and 2183 alt 5 SS events. Found 3181 RI events ========== Running the statistical part. The statistical part is done. Done. python /data/results/tools/rnaseq/mats/rMATS.4.0.2/rMATS-turbo-Linux-UCS4/rmats.py --b1 ~/bak/doc/fleming/kafasla/DKlab/mr/tzanos/rnaseq/rmats/wtIFN.txt --b2 ~/bak/doc/fleming/kafasla/DKlab/mr/tzanos/rnaseq/rmats/koIFN.txt --gtf /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf --od rmats-IFN -t paired --nthread 16 --readLength 100 --anchorLength 1 --tstat 16 There are 95495 distinct transcript ID in the gtf file There are 22375 one-transcript genes in the gtf file There are 677632 exons in the gtf file There are 13138 one-exon transcripts in the gtf file There are 12021 one-transcript genes with only one exon in the transcript Average number of transcripts per gene is 2.559501 Average number of exons per transcript is 7.095995 Average number of exons per transcript excluding one-exon tx is 8.068458 Average number of gene per geneGroup is 6.327349 ========== Done processing each gene from dictionary to compile AS events Found 28833 exon skipping events Found 3589 exon MX events Found 5957 alt SS events There are 3768 alt 3 SS events and 2189 alt 5 SS events. Found 3189 RI events ========== Running the statistical part. The statistical part is done. Done. python /data/results/tools/rnaseq/mats/rMATS.4.0.2/rMATS-turbo-Linux-UCS4/rmats.py --b1 ~/bak/doc/fleming/kafasla/DKlab/mr/tzanos/rnaseq/rmats/wtIL4.txt --b2 ~/bak/doc/fleming/kafasla/DKlab/mr/tzanos/rnaseq/rmats/koIL4.txt --gtf /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf --od rmats-IL4 -t paired --nthread 16 --readLength 100 --anchorLength 1 --tstat 16 There are 95495 distinct transcript ID in the gtf file There are 22375 one-transcript genes in the gtf file There are 677632 exons in the gtf file There are 13138 one-exon transcripts in the gtf file There are 12021 one-transcript genes with only one exon in the transcript Average number of transcripts per gene is 2.559501 Average number of exons per transcript is 7.095995 Average number of exons per transcript excluding one-exon tx is 8.068458 Average number of gene per geneGroup is 6.327349 ========== Done processing each gene from dictionary to compile AS events Found 27641 exon skipping events Found 3029 exon MX events Found 5970 alt SS events There are 3770 alt 3 SS events and 2200 alt 5 SS events. Found 3187 RI events ========== Running the statistical part. The statistical part is done. Done. for d in rmats-* do echo $d cd $d for i in *.JC.txt do echo $i awk -f ../count-sig.awk $i done cd .. done rmats-0h A3SS.MATS.JC.txt 74 A5SS.MATS.JC.txt 59 MXE.MATS.JC.txt 0 RI.MATS.JC.txt 90 SE.MATS.JC.txt 745 rmats-2h A3SS.MATS.JC.txt 60 A5SS.MATS.JC.txt 52 MXE.MATS.JC.txt 0 RI.MATS.JC.txt 56 SE.MATS.JC.txt 635 rmats-6h A3SS.MATS.JC.txt 77 A5SS.MATS.JC.txt 33 MXE.MATS.JC.txt 0 RI.MATS.JC.txt 50 SE.MATS.JC.txt 428 rmats-IFN A3SS.MATS.JC.txt 68 A5SS.MATS.JC.txt 18 MXE.MATS.JC.txt 0 RI.MATS.JC.txt 39 SE.MATS.JC.txt 353 rmats-IL4 A3SS.MATS.JC.txt 61 A5SS.MATS.JC.txt 20 MXE.MATS.JC.txt 0 RI.MATS.JC.txt 38 SE.MATS.JC.txt 469