どれもこれもうまく動かないのでふてくされてても仕方がないので、一番最新のCASHを試してみる。
javaなようなので
java -jar -Xmx8g ~/local/bin/cash_v2.1.0-alpha1/cash.jar --Case:prefix1 case.bam --Control:prefix2 Control.bam --GTF genes.gtf --Output outPath
な感じ。
まずは様子見ということで--GUIオプションを使ってGUIでファイルを指定してみる。
java -jar -Xmx8g ~/local/bin/cash_v2.1.0-alpha1/cash.jar --GUI
結果出た。すんなりスッキリ。
############################# CASH Report ############################# ====================================================================== SplicingEvent SignificantNum AllNum ====================================================================== Cassette 228 8419 Cassette_multi 25 1497 A5SS 31 2680 A3SS 19 2711 AltEnd 43 2284 AltStart 68 4373 MXE 13 410 IR 12 1156 ====================================================================== ################# Report Legend ###################################### SplicingEvent: Types of AS event Cassette: cassette exon, i.e. SE, Skipped exon Cassette_multi: mutiple adjacent Cassette exons A5SS: Alternative 5' splice site A3SS: Alternative 3' splice site AltStart: Alternative start exon AltEnd: Alternative end exon MXE: Mutually exclusive exons IR: intron retention SignificantNum: number of significantly differential AS events between samples according to FDR (false discovery rate) < 0.05 AllNum: total number of events detected between samples ######################################################################
