Read 1000000 spots for SRR3194431 Written 1000000 spots for SRR3194431 Read 1000000 spots for SRR3194429 Written 1000000 spots for SRR3194429 Read 1000000 spots for SRR3194430 Written 1000000 spots for SRR3194430 Read 1000000 spots for SRR3194428 Written 1000000 spots for SRR3194428 Read 1000000 spots for SRR3191544 Written 1000000 spots for SRR3191544 Read 1000000 spots for SRR3191542 Written 1000000 spots for SRR3191542 Read 1000000 spots for SRR3191543 Written 1000000 spots for SRR3191543 Read 1000000 spots for SRR3191545 Written 1000000 spots for SRR3191545 1000000 reads; of these: 1000000 (100.00%) were paired; of these: 60718 (6.07%) aligned concordantly 0 times 908824 (90.88%) aligned concordantly exactly 1 time 30458 (3.05%) aligned concordantly >1 times ---- 60718 pairs aligned concordantly 0 times; of these: 3540 (5.83%) aligned discordantly 1 time ---- 57178 pairs aligned 0 times concordantly or discordantly; of these: 114356 mates make up the pairs; of these: 80536 (70.43%) aligned 0 times 31259 (27.33%) aligned exactly 1 time 2561 (2.24%) aligned >1 times 95.97% overall alignment rate 1000000 reads; of these: 1000000 (100.00%) were paired; of these: 63604 (6.36%) aligned concordantly 0 times 906759 (90.68%) aligned concordantly exactly 1 time 29637 (2.96%) aligned concordantly >1 times ---- 63604 pairs aligned concordantly 0 times; of these: 3691 (5.80%) aligned discordantly 1 time ---- 59913 pairs aligned 0 times concordantly or discordantly; of these: 119826 mates make up the pairs; of these: 87746 (73.23%) aligned 0 times 29608 (24.71%) aligned exactly 1 time 2472 (2.06%) aligned >1 times 95.61% overall alignment rate 1000000 reads; of these: 1000000 (100.00%) were paired; of these: 68036 (6.80%) aligned concordantly 0 times 901429 (90.14%) aligned concordantly exactly 1 time 30535 (3.05%) aligned concordantly >1 times ---- 68036 pairs aligned concordantly 0 times; of these: 3444 (5.06%) aligned discordantly 1 time ---- 64592 pairs aligned 0 times concordantly or discordantly; of these: 129184 mates make up the pairs; of these: 85340 (66.06%) aligned 0 times 40608 (31.43%) aligned exactly 1 time 3236 (2.50%) aligned >1 times 95.73% overall alignment rate 1000000 reads; of these: 1000000 (100.00%) were paired; of these: 55865 (5.59%) aligned concordantly 0 times 914427 (91.44%) aligned concordantly exactly 1 time 29708 (2.97%) aligned concordantly >1 times ---- 55865 pairs aligned concordantly 0 times; of these: 4902 (8.77%) aligned discordantly 1 time ---- 50963 pairs aligned 0 times concordantly or discordantly; of these: 101926 mates make up the pairs; of these: 67533 (66.26%) aligned 0 times 31648 (31.05%) aligned exactly 1 time 2745 (2.69%) aligned >1 times 96.62% overall alignment rate 1000000 reads; of these: 1000000 (100.00%) were unpaired; of these: 80132 (8.01%) aligned 0 times 871653 (87.17%) aligned exactly 1 time 48215 (4.82%) aligned >1 times 91.99% overall alignment rate 1000000 reads; of these: 1000000 (100.00%) were unpaired; of these: 70989 (7.10%) aligned 0 times 877004 (87.70%) aligned exactly 1 time 52007 (5.20%) aligned >1 times 92.90% overall alignment rate 1000000 reads; of these: 1000000 (100.00%) were unpaired; of these: 71316 (7.13%) aligned 0 times 876147 (87.61%) aligned exactly 1 time 52537 (5.25%) aligned >1 times 92.87% overall alignment rate 1000000 reads; of these: 1000000 (100.00%) were unpaired; of these: 79464 (7.95%) aligned 0 times 872091 (87.21%) aligned exactly 1 time 48445 (4.84%) aligned >1 times 92.05% overall alignment rate ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.6.2 //========================== featureCounts setting ===========================\\ || || || Input files : 8 BAM files || || P SRR3191542.bam || || P SRR3191543.bam || || S SRR3194428.bam || || S SRR3194429.bam || || P SRR3191544.bam || || P SRR3191545.bam || || S SRR3194430.bam || || S SRR3194431.bam || || || || Output file : counts.txt || || Summary : counts.txt.summary || || Annotation : Homo_sapiens.GRCh38.96.chr.gtf (GTF) || || Dir for temp files : ./ || || || || Threads : 1 || || Level : meta-feature level || || Paired-end : no || || Multimapping reads : not counted || || Multi-overlapping reads : not counted || || Min overlapping bases : 1 || || || \\===================== http://subread.sourceforge.net/ ======================// //================================= Running ==================================\\ || || || Load annotation file Homo_sapiens.GRCh38.96.chr.gtf ... || || Features : 1278818 || || Meta-features : 57316 || || Chromosomes/contigs : 25 || || || || Process BAM file SRR3191542.bam... || || Paired-end reads are included. || || Assign reads to features... || || Total reads : 2108533 || || Successfully assigned reads : 1470505 (69.7%) || || Running time : 0.05 minutes || || || || Process BAM file SRR3191543.bam... || || Paired-end reads are included. || || Assign reads to features... || || Total reads : 2114924 || || Successfully assigned reads : 1466905 (69.4%) || || Running time : 0.05 minutes || || || || Process BAM file SRR3194428.bam... || || Single-end reads are included. || || Assign reads to features... || || Total reads : 1093016 || || Successfully assigned reads : 681166 (62.3%) || || Running time : 0.03 minutes || || || || Process BAM file SRR3194429.bam... || || Single-end reads are included. || || Assign reads to features... || || Total reads : 1095231 || || Successfully assigned reads : 688354 (62.9%) || || Running time : 0.03 minutes || || || || Process BAM file SRR3191544.bam... || || Paired-end reads are included. || || Assign reads to features... || || Total reads : 2123250 || || Successfully assigned reads : 1433818 (67.5%) || || Running time : 0.05 minutes || || || || Process BAM file SRR3191545.bam... || || Paired-end reads are included. || || Assign reads to features... || || Total reads : 2118590 || || Successfully assigned reads : 1438675 (67.9%) || || Running time : 0.05 minutes || || || || Process BAM file SRR3194430.bam... || || Single-end reads are included. || || Assign reads to features... || || Total reads : 1092372 || || Successfully assigned reads : 663829 (60.8%) || || Running time : 0.03 minutes || || || || Process BAM file SRR3194431.bam... || || Single-end reads are included. || || Assign reads to features... || || Total reads : 1090920 || || Successfully assigned reads : 667752 (61.2%) || || Running time : 0.03 minutes || || || || Read assignment finished. || || || || Summary of counting results can be found in file "counts.txt.summary" || || || \\===================== http://subread.sourceforge.net/ ======================// Loading required package: BiocGenerics Loading required package: parallel Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:parallel’: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: anyDuplicated, append, as.data.frame, basename, cbind, colMeans, colnames, colSums, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans, rownames, rowSums, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: locfit locfit 1.5-9.1 2013-03-22 Loading required package: lattice Welcome to 'DESeq'. For improved performance, usability and functionality, please consider migrating to 'DESeq2'. Attaching package: ‘gplots’ The following object is masked from ‘package:stats’: lowess