>>>> [1A(Untreated PMNs) vs 1B(PMNs+IRA plasma)] PAIR >>>> [3A(Untreated PMNs) vs 3B(PMNs+IRA plasma)] PAIR >>>> [4A(Untreated PMNs) vs 4B(PMNs+IRA plasma)] PAIR >>>> >>>> [5E(Untreated PMNs) vs 5F(PMNs+polyP)] PAIR >>>> [6E(Untreated PMNs) vs 6F(PMNs+polyP)] PAIR >>>> [8E(Untreated PMNs) vs 8F(PMNs+polyP)] PAIR Contrast: UntrPMN_vs_PMNsIRAplasma , pairs: 15 DSt3R1 /data/images/proton2/run409/DrStakos/DSt3R1-1A-UntrPMNs.bam UntrPMNs134 single yes 28 DSt3R2 /data/images/proton2/run409/DrStakos/DSt3R2-1B-PMNsIRAplasma.bam PMNsIRAplasma single yes 14 DSt3R5 /data/images/proton2/run409/DrStakos/DSt3R5-3A-UntrPMNs.bam UntrPMNs134 single yes 18 DSt3R6 /data/images/proton2/run409/DrStakos/DSt3R6-3B-PMNsIRAplasma.bam PMNsIRAplasma single yes 30 DSt3R9 /data/images/proton2/run409/DrStakos/DSt3R9-4A-UntrPMNs.bam UntrPMNs134 single yes 7 DSt3R10 /data/images/proton2/run409/DrStakos/DSt3R10-4B-PMNsIRAplasma.bam PMNsIRAplasma single yes Contrast: UntrPMN_vs_PMNspolyP , pairs: 23 DSt3R13 /data/images/proton2/run409/DrStakos/DSt3R13-5E-UntrPMNs.bam UntrPMNs568 single yes 27 DSt3R14 /data/images/proton2/run409/DrStakos/DSt3R14-5F-PMNspolyP.bam PMNspolyP single yes 16 DSt3R19 /data/images/proton2/run409/DrStakos/DSt3R19-6E-UntrPMNs.bam UntrPMNs568 single yes 20 DSt3R20 /data/images/proton2/run409/DrStakos/DSt3R20-6F-PMNspolyP.bam PMNspolyP single yes 13 DSt3R25 /data/images/proton2/run409/DrStakos/DSt3R25-8E-UntrPMNs.bam UntrPMNs568 single yes 17 DSt3R26 /data/images/proton2/run409/DrStakos/DSt3R26-8F-PMNspolyP.bam PMNspolyP single yes Contrast: UntrPMN_vs_PMNsIRAplasmaIL29 , pairs: 15 DSt3R1 /data/images/proton2/run409/DrStakos/DSt3R1-1A-UntrPMNs.bam UntrPMNs134 single yes 10 DSt3R4 /data/images/proton2/run409/DrStakos/DSt3R4-1D-PMNsIRAplasmaIL29.bam PMNsIRAplasmaIL29 single yes 14 DSt3R5 /data/images/proton2/run409/DrStakos/DSt3R5-3A-UntrPMNs.bam UntrPMNs134 single yes 26 DSt3R8 /data/images/proton2/run409/DrStakos/DSt3R8-3D-PMNsIRAplasmaIL29.bam PMNsIRAplasmaIL29 single yes 30 DSt3R9 /data/images/proton2/run409/DrStakos/DSt3R9-4A-UntrPMNs.bam UntrPMNs134 single yes 19 DSt3R12 /data/images/proton2/run409/DrStakos/DSt3R12-4D-PMNsIRAplasmaIL29.bam PMNsIRAplasmaIL29 single yes "genes" "logFC" "logCPM" "F" "PValue" "FDR" "49491" "ENSMUSG00000097971" -3.40143614434846 10.9776634097239 22.0796962703195 2.6188451631729e-06 0.140896488623865 "DSt3R1.1A.UntrPMNs.bam" "DSt3R2.1B.PMNsIRAplasma.bam" "DSt3R5.3A.UntrPMNs.bam" "DSt3R6.3B.PMNsIRAplasma.bam" "DSt3R9.4A.UntrPMNs.bam" "DSt3R10.4B.PMNsIRAplasma.bam" 49.232587049368 1862.11822325012 165.412290133157 3025.67274226604 2279.77764360517 4608.95678286983 (/ 1862 49.2) 37.84552845528455 (/ 3025 165.4) 18.28899637243047 (/ 4608.95 2279.7) 2.0217353160503575 2^3.4 = 10.55 (/ (+ 38 18 2) 3.0) 19.333333333333332 for i in *bam do echo $i /data/results/tools/rnaseq/subread/subread-1.5.2-source/bin/featureCounts -M -s 1 -T 4 -a /data/results/reference/mmu/Mus_musculus.GRCm38.92.exons.gtf -o $i".cnt" $i done /data/results/tools/rnaseq/subread/subread-1.5.2-source/bin/featureCounts -M -s 1 -T 4 -a /data/results/reference/hg19/Homo_sapiens.GRCh38.84.chr.gtf -o gene_counts.txt DSt3R10-4B-PMNsIRAplasma.bam DSt3R17-5I-PMNsTIC.bam DSt3R24-6J-PMNsIL29.bam DSt3R4-1D-PMNsIRAplasmaIL29.bam DSt3R11-4C-PMNsIRAplasmaTIC.bam DSt3R18-5J-PMNsIL29.bam DSt3R25-8E-UntrPMNs.bam DSt3R5-3A-UntrPMNs.bam DSt3R1-1A-UntrPMNs.bam DSt3R19-6E-UntrPMNs.bam DSt3R26-8F-PMNspolyP.bam DSt3R6-3B-PMNsIRAplasma.bam DSt3R12-4D-PMNsIRAplasmaIL29.bam DSt3R20-6F-PMNspolyP.bam DSt3R27-8G-PMNspolyPTIC.bam DSt3R7-3C-PMNsIRAplasmaTIC.bam DSt3R13-5E-UntrPMNs.bam DSt3R21-6G-PMNspolyPTIC.bam DSt3R28-8H-PMNspolyPIL29.bam DSt3R8-3D-PMNsIRAplasmaIL29.bam DSt3R14-5F-PMNspolyP.bam DSt3R2-1B-PMNsIRAplasma.bam DSt3R29-8I-PMNsTIC.bam DSt3R9-4A-UntrPMNs.bam DSt3R15-5G-PMNspolyPTIC.bam DSt3R22-6H-PMNspolyPIL29.bam DSt3R30-8J-PMNsIL29.bam DSt3R16-5H-PMNspolyPIL29.bam DSt3R23-6I-PMNsTIC.bam DSt3R3-1C-PMNsIRAplasmaTIC.bam #log in featureCounts.log #mmu #/data/results/tools/rnaseq/subread/subread-1.5.2-source/bin/featureCounts -M -s 1 -T 4 -a /data/results/reference/mmu/Mus_musculus.GRCm38.92.exons.gtf -o gene_counts.txt-mmu DSt3R10-4B-PMNsIRAplasma.bam DSt3R17-5I-PMNsTIC.bam DSt3R24-6J-PMNsIL29.bam DSt3R4-1D-PMNsIRAplasmaIL29.bam DSt3R11-4C-PMNsIRAplasmaTIC.bam DSt3R18-5J-PMNsIL29.bam DSt3R25-8E-UntrPMNs.bam DSt3R5-3A-UntrPMNs.bam DSt3R1-1A-UntrPMNs.bam DSt3R19-6E-UntrPMNs.bam DSt3R26-8F-PMNspolyP.bam DSt3R6-3B-PMNsIRAplasma.bam DSt3R12-4D-PMNsIRAplasmaIL29.bam DSt3R20-6F-PMNspolyP.bam DSt3R27-8G-PMNspolyPTIC.bam DSt3R7-3C-PMNsIRAplasmaTIC.bam DSt3R13-5E-UntrPMNs.bam DSt3R21-6G-PMNspolyPTIC.bam DSt3R28-8H-PMNspolyPIL29.bam DSt3R8-3D-PMNsIRAplasmaIL29.bam DSt3R14-5F-PMNspolyP.bam DSt3R2-1B-PMNsIRAplasma.bam DSt3R29-8I-PMNsTIC.bam DSt3R9-4A-UntrPMNs.bam DSt3R15-5G-PMNspolyPTIC.bam DSt3R22-6H-PMNspolyPIL29.bam DSt3R30-8J-PMNsIL29.bam DSt3R16-5H-PMNspolyPIL29.bam DSt3R23-6I-PMNsTIC.bam DSt3R3-1C-PMNsIRAplasmaTIC.bam reczko@estia:/mnt/scratch/dermitzakis$ ls htseq/*counts.txt > /tmp/foo reczko@estia:/mnt/scratch/dermitzakis$ awk -f /data/results/tools/rnaseq/collect-gene-count-per-sample-from-htseq1.awk /tmp/foo > htseq/all-gene-counts-htseq.txt