#@ per-gene annotation Martin Reczko Mon, Jun 11, 2018 at 8:04 PM To: Margarita Chatzimike , Giorgos Giagkas Dear Margarita and George, the per-gene processing results as discussed today are at /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d For now there is no NMD distinction. The region code is: 1=3utr,2=5utr,3=cds,4=other. sh-clusters-0h.gt0.25TtoC2.plus.noIGG.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno.bed.genomic2.bed.collapsed.best.per-gene-exons.bed 10172 3utr 1640 5utr 9230 cds 1625 other 1st max: 3utr 1037 5utr 588 cds 0 2nd max: 3utr 0 5utr 49 cds 1576 sh-clusters-2h.gt0.25TtoC2.plus.noIGG.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno.bed.genomic2.bed.collapsed.best.per-gene-exons.bed 6963 3utr 875 5utr 7352 cds 1182 other 1st max: 3utr 807 5utr 375 cds 0 2nd max: 3utr 0 5utr 24 cds 1158 sh-clusters-6h.gt0.25TtoC2.plus.noIGG.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno.bed.genomic2.bed.collapsed.best.per-gene-exons.bed 10528 3utr 2119 5utr 11366 cds 2046 other 1st max: 3utr 1314 5utr 732 cds 0 2nd max: 3utr 0 5utr 39 cds 2007 sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.flt.anno.bed.genomic2.bed.collapsed.best.per-gene-exons.bed 3509 3utr 622 5utr 3916 cds 666 other 1st max: 3utr 399 5utr 267 cds 0 2nd max: 3utr 0 5utr 13 cds 653 sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.flt.anno.bed.genomic2.bed.collapsed.best.per-gene-exons.bed 5353 3utr 783 5utr 5818 cds 997 other 1st max: 3utr 663 5utr 334 cds 0 2nd max: 3utr 0 5utr 21 cds 976 clusters in introns (both PGC/ncRNA): 1111 sh-clusters-0h.gt0.25TtoC2.plus.noIGG.flt.srt.intersection-all.bed3-1kIntrons.merged.maxAvg.bed.anno.bed.genomic2.bed.collapsed.anno2.intron 54664 sh-clusters-0h.gt0.25TtoC2.plus.noIGG.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno.bed.genomic2.bed.collapsed.anno2.intron 586 sh-clusters-2h.gt0.25TtoC2.plus.noIGG.flt.srt.intersection-all.bed3-1kIntrons.merged.maxAvg.bed.anno.bed.genomic2.bed.collapsed.anno2.intron 40588 sh-clusters-2h.gt0.25TtoC2.plus.noIGG.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno.bed.genomic2.bed.collapsed.anno2.intron 1678 sh-clusters-6h.gt0.25TtoC2.plus.noIGG.flt.srt.intersection-all.bed3-1kIntrons.merged.maxAvg.bed.anno.bed.genomic2.bed.collapsed.anno2.intron 61469 sh-clusters-6h.gt0.25TtoC2.plus.noIGG.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno.bed.genomic2.bed.collapsed.anno2.intron 20414 sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.flt.anno.bed.genomic2.bed.collapsed.anno2.intron 32019 sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.flt.anno.bed.genomic2.bed.collapsed.anno2.intron clusters in exons of ncRNA: 105 sh-clusters-0h.gt0.25TtoC2.plus.noIGG.flt.srt.intersection-all.bed3-1kIntrons.merged.maxAvg.bed.anno.bed.genomic2.bed.collapsed.anno2.exon.ncRNA 5255 sh-clusters-0h.gt0.25TtoC2.plus.noIGG.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno.bed.genomic2.bed.collapsed.anno2.exon.ncRNA 52 sh-clusters-2h.gt0.25TtoC2.plus.noIGG.flt.srt.intersection-all.bed3-1kIntrons.merged.maxAvg.bed.anno.bed.genomic2.bed.collapsed.anno2.exon.ncRNA 3959 sh-clusters-2h.gt0.25TtoC2.plus.noIGG.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno.bed.genomic2.bed.collapsed.anno2.exon.ncRNA 135 sh-clusters-6h.gt0.25TtoC2.plus.noIGG.flt.srt.intersection-all.bed3-1kIntrons.merged.maxAvg.bed.anno.bed.genomic2.bed.collapsed.anno2.exon.ncRNA 5922 sh-clusters-6h.gt0.25TtoC2.plus.noIGG.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno.bed.genomic2.bed.collapsed.anno2.exon.ncRNA 2023 sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.flt.anno.bed.genomic2.bed.collapsed.anno2.exon.ncRNA 3154 sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.flt.anno.bed.genomic2.bed.collapsed.anno2.exon.ncRNA #@ made with /data/images/proton/DKlab/mr/parclip/paralyzer/README-paralyzer15.txt per-gene annotation Martin Reczko Tue, Jun 12, 2018 at 8:42 PM To: Margarita Chatzimike , Giorgos Giagkas Dear Margarita and George, the additional (3utr/5utr/cds) annotation per cluster is in the lists below (path /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d). For clusters in PCGs: 10995 sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.genomic2.bed.collapsed.best.per-gene-exons.bed.3utr.bed 2230 sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.genomic2.bed.collapsed.best.per-gene-exons.bed.5utr.bed 10568 sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.genomic2.bed.collapsed.best.per-gene-exons.bed.cds.bed 7777 sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.genomic2.bed.collapsed.best.per-gene-exons.bed.3utr.bed 1266 sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.genomic2.bed.collapsed.best.per-gene-exons.bed.5utr.bed 8460 sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.genomic2.bed.collapsed.best.per-gene-exons.bed.cds.bed 11643 sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.genomic2.bed.collapsed.best.per-gene-exons.bed.3utr.bed 2845 sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.genomic2.bed.collapsed.best.per-gene-exons.bed.5utr.bed 13144 sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.genomic2.bed.collapsed.best.per-gene-exons.bed.cds.bed 3477 sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.genomic2.bed.collapsed.best.per-gene-exons.bed.3utr.bed 798 sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.genomic2.bed.collapsed.best.per-gene-exons.bed.5utr.bed 3965 sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.genomic2.bed.collapsed.best.per-gene-exons.bed.cds.bed 5927 sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.genomic2.bed.collapsed.best.per-gene-exons.bed.3utr.bed 1117 sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.genomic2.bed.collapsed.best.per-gene-exons.bed.5utr.bed 6657 sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.genomic2.bed.collapsed.best.per-gene-exons.bed.cds.bed For clusters in introns: 447 sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.genomic2.bed.collapsed.anno2.intron.3utr.bed 501 sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.genomic2.bed.collapsed.anno2.intron.5utr.bed 3198 sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.genomic2.bed.collapsed.anno2.intron.cds.bed 384 sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.genomic2.bed.collapsed.anno2.intron.3utr.bed 406 sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.genomic2.bed.collapsed.anno2.intron.5utr.bed 2783 sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.genomic2.bed.collapsed.anno2.intron.cds.bed 468 sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.genomic2.bed.collapsed.anno2.intron.3utr.bed 588 sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.genomic2.bed.collapsed.anno2.intron.5utr.bed 3634 sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.genomic2.bed.collapsed.anno2.intron.cds.bed 124 sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.genomic2.bed.collapsed.anno2.intron.3utr.bed 178 sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.genomic2.bed.collapsed.anno2.intron.5utr.bed 974 sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.genomic2.bed.collapsed.anno2.intron.cds.bed 215 sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.genomic2.bed.collapsed.anno2.intron.3utr.bed 253 sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.genomic2.bed.collapsed.anno2.intron.5utr.bed 1480 sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.genomic2.bed.collapsed.anno2.intron.cds.bed BW, Martin per-gene annotation Martin Reczko Wed, Jun 13, 2018 at 5:10 PM To: Margarita Chatzimike , Giorgos Giagkas Please reload the secondary intron annotation, the minus strand was missing: PCG clusters overlapping with introns: 13417 sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.genomic2.bed.collapsed.best.per-gene-exons.bed.intron.bed 9825 sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.genomic2.bed.collapsed.best.per-gene-exons.bed.intron.bed 15374 sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.genomic2.bed.collapsed.best.per-gene-exons.bed.intron.bed 4619 sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.genomic2.bed.collapsed.best.per-gene-exons.bed.intron.bed 7644 sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.genomic2.bed.collapsed.best.per-gene-exons.bed.intron.bed ncRNA clusters overlapping with introns: 3597 sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.genomic2.bed.collapsed.anno2.exon.ncRNA.intron.bed 2700 sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.genomic2.bed.collapsed.anno2.exon.ncRNA.intron.bed 4048 sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.genomic2.bed.collapsed.anno2.exon.ncRNA.intron.bed 1217 sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.genomic2.bed.collapsed.anno2.exon.ncRNA.intron.bed 2190 sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.genomic2.bed.collapsed.anno2.exon.ncRNA.intron.bed #@ Dear Margarita and George, the per-gene processing results as discussed today are at /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d: sh-clusters-0h.gt0.25TtoC2.plus.noIGG.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno.bed.genomic2.bed.collapsed.best.per-gene-exons.bed 10172 3utr 1640 5utr 9230 cds 1625 other 1st max: 3utr 1037 5utr 588 cds 0 2nd max: 3utr 0 5utr 49 cds 1576 sh-clusters-2h.gt0.25TtoC2.plus.noIGG.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno.bed.genomic2.bed.collapsed.best.per-gene-exons.bed 6963 3utr 875 5utr 7352 cds 1182 other 1st max: 3utr 807 5utr 375 cds 0 2nd max: 3utr 0 5utr 24 cds 1158 sh-clusters-6h.gt0.25TtoC2.plus.noIGG.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno.bed.genomic2.bed.collapsed.best.per-gene-exons.bed 10528 3utr 2119 5utr 11366 cds 2046 other 1st max: 3utr 1314 5utr 732 cds 0 2nd max: 3utr 0 5utr 39 cds 2007 sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.flt.anno.bed.genomic2.bed.collapsed.best.per-gene-exons.bed 3509 3utr 622 5utr 3916 cds 666 other 1st max: 3utr 399 5utr 267 cds 0 2nd max: 3utr 0 5utr 13 cds 653 sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.flt.anno.bed.genomic2.bed.collapsed.best.per-gene-exons.bed 5353 3utr 783 5utr 5818 cds 997 other 1st max: 3utr 663 5utr 334 cds 0 2nd max: 3utr 0 5utr 21 cds 976 clusters in introns (both PGC/ncRNA): 1111 sh-clusters-0h.gt0.25TtoC2.plus.noIGG.flt.srt.intersection-all.bed3-1kIntrons.merged.maxAvg.bed.anno.bed.genomic2.bed.collapsed.anno2.intron 54664 sh-clusters-0h.gt0.25TtoC2.plus.noIGG.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno.bed.genomic2.bed.collapsed.anno2.intron 586 sh-clusters-2h.gt0.25TtoC2.plus.noIGG.flt.srt.intersection-all.bed3-1kIntrons.merged.maxAvg.bed.anno.bed.genomic2.bed.collapsed.anno2.intron 40588 sh-clusters-2h.gt0.25TtoC2.plus.noIGG.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno.bed.genomic2.bed.collapsed.anno2.intron 1678 sh-clusters-6h.gt0.25TtoC2.plus.noIGG.flt.srt.intersection-all.bed3-1kIntrons.merged.maxAvg.bed.anno.bed.genomic2.bed.collapsed.anno2.intron 61469 sh-clusters-6h.gt0.25TtoC2.plus.noIGG.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno.bed.genomic2.bed.collapsed.anno2.intron 20414 sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.flt.anno.bed.genomic2.bed.collapsed.anno2.intron 32019 sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.flt.anno.bed.genomic2.bed.collapsed.anno2.intron clusters in exons of ncRNA: 105 sh-clusters-0h.gt0.25TtoC2.plus.noIGG.flt.srt.intersection-all.bed3-1kIntrons.merged.maxAvg.bed.anno.bed.genomic2.bed.collapsed.anno2.exon.ncRNA 5255 sh-clusters-0h.gt0.25TtoC2.plus.noIGG.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno.bed.genomic2.bed.collapsed.anno2.exon.ncRNA 52 sh-clusters-2h.gt0.25TtoC2.plus.noIGG.flt.srt.intersection-all.bed3-1kIntrons.merged.maxAvg.bed.anno.bed.genomic2.bed.collapsed.anno2.exon.ncRNA 3959 sh-clusters-2h.gt0.25TtoC2.plus.noIGG.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno.bed.genomic2.bed.collapsed.anno2.exon.ncRNA 135 sh-clusters-6h.gt0.25TtoC2.plus.noIGG.flt.srt.intersection-all.bed3-1kIntrons.merged.maxAvg.bed.anno.bed.genomic2.bed.collapsed.anno2.exon.ncRNA 5922 sh-clusters-6h.gt0.25TtoC2.plus.noIGG.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno.bed.genomic2.bed.collapsed.anno2.exon.ncRNA 2023 sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.flt.anno.bed.genomic2.bed.collapsed.anno2.exon.ncRNA 3154 sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.flt.anno.bed.genomic2.bed.collapsed.anno2.exon.ncRNA PCG clusters overlapping with introns: 13417 sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.genomic2.bed.collapsed.best.per-gene-exons.bed.intron.bed 9825 sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.genomic2.bed.collapsed.best.per-gene-exons.bed.intron.bed 15374 sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.genomic2.bed.collapsed.best.per-gene-exons.bed.intron.bed 4619 sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.genomic2.bed.collapsed.best.per-gene-exons.bed.intron.bed 7644 sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.genomic2.bed.collapsed.best.per-gene-exons.bed.intron.bed ncRNA clusters overlapping with introns: 3597 sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.genomic2.bed.collapsed.anno2.exon.ncRNA.intron.bed 2700 sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.genomic2.bed.collapsed.anno2.exon.ncRNA.intron.bed 4048 sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.genomic2.bed.collapsed.anno2.exon.ncRNA.intron.bed 1217 sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.genomic2.bed.collapsed.anno2.exon.ncRNA.intron.bed 2190 sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.genomic2.bed.collapsed.anno2.exon.ncRNA.intron.bed #@ with correct filter sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.genomic2.bed.collapsed.best.per-gene-exons.bed 3724 3utr 623 5utr 4348 cds 735 other 1st max: 3utr 489 5utr 246 cds 0 2nd max: 3utr 0 5utr 15 cds 720 sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.genomic2.bed.collapsed.best.per-gene-exons.bed 2342 3utr 461 5utr 2687 cds 491 other 1st max: 3utr 298 5utr 193 cds 0 2nd max: 3utr 0 5utr 9 cds 482 sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.genomic2.bed.collapsed.best.per-gene-exons.bed 7410 3utr 1703 5utr 8890 cds 1591 other 1st max: 3utr 1028 5utr 563 cds 0 2nd max: 3utr 0 5utr 30 cds 1561 sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.genomic2.bed.collapsed.best.per-gene-exons.bed 5248 3utr 711 5utr 5982 cds 986 other 1st max: 3utr 669 5utr 317 cds 0 2nd max: 3utr 0 5utr 22 cds 964 sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.genomic2.bed.collapsed.best.per-gene-exons.bed 6638 3utr 1238 5utr 6933 cds 1217 other 1st max: 3utr 760 5utr 457 cds 0 2nd max: 3utr 0 5utr 37 cds 1180 2nd annotation, clusters in PCGs: 7398 sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.genomic2.bed.collapsed.best.per-gene-exons.bed.3utr.bed 1732 sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.genomic2.bed.collapsed.best.per-gene-exons.bed.5utr.bed 8133 sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.genomic2.bed.collapsed.best.per-gene-exons.bed.cds.bed 9720 sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.genomic2.bed.collapsed.best.per-gene-exons.bed.intron.bed 5917 sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.genomic2.bed.collapsed.best.per-gene-exons.bed.3utr.bed 1050 sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.genomic2.bed.collapsed.best.per-gene-exons.bed.5utr.bed 6960 sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.genomic2.bed.collapsed.best.per-gene-exons.bed.cds.bed 7776 sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.genomic2.bed.collapsed.best.per-gene-exons.bed.intron.bed 8438 sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.genomic2.bed.collapsed.best.per-gene-exons.bed.3utr.bed 2296 sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.genomic2.bed.collapsed.best.per-gene-exons.bed.5utr.bed 10468 sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.genomic2.bed.collapsed.best.per-gene-exons.bed.cds.bed 11794 sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.genomic2.bed.collapsed.best.per-gene-exons.bed.intron.bed 2640 sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.genomic2.bed.collapsed.best.per-gene-exons.bed.3utr.bed 663 sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.genomic2.bed.collapsed.best.per-gene-exons.bed.5utr.bed 3175 sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.genomic2.bed.collapsed.best.per-gene-exons.bed.cds.bed 3612 sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.genomic2.bed.collapsed.best.per-gene-exons.bed.intron.bed 4213 sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.genomic2.bed.collapsed.best.per-gene-exons.bed.3utr.bed 884 sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.genomic2.bed.collapsed.best.per-gene-exons.bed.5utr.bed 5079 sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.genomic2.bed.collapsed.best.per-gene-exons.bed.cds.bed 5674 sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.genomic2.bed.collapsed.best.per-gene-exons.bed.intron.bed 2nd annotation, ncRNA clusters overlapping with introns: 2523 sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.genomic2.bed.collapsed.anno2.exon.ncRNA.intron.bed 2084 sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.genomic2.bed.collapsed.anno2.exon.ncRNA.intron.bed 2985 sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.genomic2.bed.collapsed.anno2.exon.ncRNA.intron.bed 940 sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.genomic2.bed.collapsed.anno2.exon.ncRNA.intron.bed 1543 sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.genomic2.bed.collapsed.anno2.exon.ncRNA.intron.bed 2nd annotation, clusters in introns (both PGC/ncRNA): 292 sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.genomic2.bed.collapsed.anno2.intron.3utr.bed 360 sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.genomic2.bed.collapsed.anno2.intron.5utr.bed 2193 sh-clusters-0h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.genomic2.bed.collapsed.anno2.intron.cds.bed 291 sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.genomic2.bed.collapsed.anno2.intron.3utr.bed 286 sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.genomic2.bed.collapsed.anno2.intron.5utr.bed 2034 sh-clusters-2h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.genomic2.bed.collapsed.anno2.intron.cds.bed 329 sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.genomic2.bed.collapsed.anno2.intron.3utr.bed 426 sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.genomic2.bed.collapsed.anno2.intron.5utr.bed 2569 sh-clusters-6h.gt0.25TtoC2.plus.noIGG.f.flt.srt.union.bed3-1kIntrons.merged.maxAvg.bed.anno1.bed.genomic2.bed.collapsed.anno2.intron.cds.bed 94 sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.genomic2.bed.collapsed.anno2.intron.3utr.bed 149 sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.genomic2.bed.collapsed.anno2.intron.5utr.bed 752 sh-clusters-IFN.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.genomic2.bed.collapsed.anno2.intron.cds.bed 167 sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.genomic2.bed.collapsed.anno2.intron.3utr.bed 202 sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.genomic2.bed.collapsed.anno2.intron.5utr.bed 1137 sh-clusters-IL4.txt2-1kIntrons.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.f.flt.anno1.bed.genomic2.bed.collapsed.anno2.intron.cds.bed