http://bioinf.wehi.edu.au/subread-package/SubreadUsersGuide.pdf
を参考に。
$ ~/local/bin/subread-1.5.2-MaxOSX-x86_64/bin/featureCounts -T 4 -a ~/expression/Homo_sapiens/NCBI/build37.2/Annotation/Archives/archive-2014-06-02-13-47-29/Genes/genes.gtf -t exon -g gene_id -o counts.txt SRR1234567_th.bam
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.5.2
//========================== featureCounts setting ===========================\\
|| ||
|| Input files : 1 BAM file ||
|| P SRR1234567_th.bam ||
|| ||
|| Output file : counts.txt ||
|| Summary : counts.txt.summary ||
|| Annotation : ~/expression/Homo_sapiens/NCBI/bu ... ||
|| Dir for temp files : ./ ||
|| ||
|| Threads : 4 ||
|| Level : meta-feature level ||
|| Paired-end : no ||
|| Strand specific : no ||
|| Multimapping reads : not counted ||
|| Multi-overlapping reads : not counted ||
|| Min overlapping bases : 1 ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//================================= Running ==================================\\
|| ||
|| Load annotation file ~/expression/Homo_sapiens/NCBI/build37 ... ||
|| Features : 376868 ||
|| Meta-features : 25559 ||
|| Chromosomes/contigs : 50 ||
|| ||
|| Process BAM file SRR1234567_th.bam... ||
|| Paired-end reads are included. ||
|| Assign reads to features... ||
|| Total reads : 15002179 ||
|| Successfully assigned reads : 8804493 (58.7%) ||
|| Running time : 0.14 minutes ||
|| ||
|| Read assignment finished. ||
|| ||
|| Summary of counting results can be found in file "counts.txt" ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//tophatで使ったannotationのgtfファイルをそのまま使い、tophatで出力されたBAMファイルをかけてみた。
出力されたファイルはcounts.txtとcounts.txt.summaryの２つ。かかった時間は一瞬。
Paired-end :noはおかしいので設定見直し。
