./pip-pgg.sh cd /data/images/proton/DKlab/polysomes/ /data/images/proton/DKlab/polysomes/polysome-normalized-DEseq2-diff-exp2.r reczko@max:~/bak/doc/fleming/kafasla/DKlab/mr/Polysomes/www$ /data/images/proton/runStringtie-mm9.sh reczko@max:~/bak/doc/fleming/kafasla/DKlab/mr/Polysomes/www$ ./pip.sh &> pip.log & /data/images/proton/DKlab/mr/Polysomes/www/pip-merge-RNAandPolysomSeq.sh reczko@max:~/bak/doc/fleming/kafasla/DKlab/mr/Polysomes/www$ /data/results/tools/rnaseq/stringtie/stringtie-master/prepDE.py /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedwt01pos.sorted.bam -p 8 -e -B -o ballgown/wt01/wt01.merged.gtf -G merged.gtf /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedwt02pos.sorted.bam -p 8 -e -B -o ballgown/wt02/wt02.merged.gtf -G merged.gtf /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedwt21pos.bam -p 8 -e -B -o ballgown/wt21/wt21.merged.gtf -G merged.gtf /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedwt22pos.bam -p 8 -e -B -o ballgown/wt22/wt22.merged.gtf -G merged.gtf /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedwt61pos.bam -p 8 -e -B -o ballgown/wt61/wt61.merged.gtf -G merged.gtf /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedwt62pos.bam -p 8 -e -B -o ballgown/wt62/wt62.merged.gtf -G merged.gtf /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedwtIFN1pos.bam -p 8 -e -B -o ballgown/wtIFN1/wtIFN1.merged.gtf -G merged.gtf /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedwtIFN2pos.bam -p 8 -e -B -o ballgown/wtIFN2/wtIFN2.merged.gtf -G merged.gtf /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedwt01IL4pos.bam -p 8 -e -B -o ballgown/wt01IL4/wt01IL4.merged.gtf -G merged.gtf /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedwt02IL4pos.bam -p 8 -e -B -o ballgown/wt02IL4/wt02IL4.merged.gtf -G merged.gtf /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedKo01pos.sorted.bam -p 8 -e -B -o ballgown/Ko01/Ko01.merged.gtf -G merged.gtf /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedKo02pos.sorted.bam -p 8 -e -B -o ballgown/Ko02/Ko02.merged.gtf -G merged.gtf /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedKO21pos.bam -p 8 -e -B -o ballgown/KO21/KO21.merged.gtf -G merged.gtf /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedKO22pos.bam -p 8 -e -B -o ballgown/KO22/KO22.merged.gtf -G merged.gtf /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedKo61pos.bam -p 8 -e -B -o ballgown/Ko61/Ko61.merged.gtf -G merged.gtf /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedKo62pos.bam -p 8 -e -B -o ballgown/Ko62/Ko62.merged.gtf -G merged.gtf /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedKOIFN1pos.bam -p 8 -e -B -o ballgown/KOIFN1/KOIFN1.merged.gtf -G merged.gtf /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedKOIFN2pos.bam -p 8 -e -B -o ballgown/KOIFN2/KOIFN2.merged.gtf -G merged.gtf /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedKo1IL4pos.bam -p 8 -e -B -o ballgown/Ko1IL4/Ko1IL4.merged.gtf -G merged.gtf /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedKo2IL4pos.bam -p 8 -e -B -o ballgown/Ko2IL4/Ko2IL4.merged.gtf -G merged.gtf 1 KO21 2 KO22 3 KOIFN1 4 KOIFN2 5 KO_0h_replicate_I 6 KO_0h_replicate_II 7 KO_2h_replicate_I 8 KO_2h_replicate_II 9 KO_6h_replicate_I 10 KO_6h_replicate_II 11 KO_IFN-gamma_replicate_I 12 KO_IFN-gamma_replicate_II 13 KO_IL4_replicate_I 14 KO_IL4_replicate_II 15 Ko01 16 Ko02 17 Ko1IL4 18 Ko2IL4 19 Ko61 20 Ko62 21 WT_0h_replicate_I 22 WT_0h_replicate_II_ 23 WT_2h_replicate_I 24 WT_2h_replicate_II 25 WT_6h_replicate_I 26 WT_6h_replicate_II 27 WT_IFN-gamma_replicate_I 28 WT_IFN-gamma_replicate_II 29 WT_IL4_replicate_I 30 WT_IL4_replicate_II 31 wt01 32 wt01IL4 33 wt02 34 wt02IL4 35 wt21 36 wt22 37 wt61 38 wt62 39 wtIFN1 40 wtIFN2 ls e*Ex*csv > all-edger-results.txt awk -f addGeneToEdger.awk all-edger-results.txt edgeRtranscriptsExpr-0h-RNAseq.withGID.csv geneName geneID transcriptID "logFC" "logCPM" "PValue" "FDR" "Ko01" "Ko02" "wt01" "wt02" "Elavl1" "MSTRG.18981" "ENSMUST00000098950" 2.6426820818034 4.30768216058649 0.03245128473768 0.52613576528407 6.09682648609755 4.82453483986407 41.5937850859715 26.6204910817268