> ~/project/RNA-seq/count/GeneMat.txt 3.2 run-ebseq 调用EBseq进行检验 ~/software/rsem/rsem-run-ebseq \ GeneMat.txt 2,2,2,2 GeneMat.results #2,2,2,2表示4个condition, 每个condition有两个重复;顺序要和3.1中输入文件表示的condition的顺序一致 #会得到三个文件 GeneMat.results.condmeans GeneMa...
$ rsem-plot-model sample.name sample.name.diagnostic.pdf (可选,看一些统计) 2. 差异表达: $ rsem-generate-data-matrix sampleA.results sampleB.results ... > samples.matrix $ rsem-run-ebseq samples.matrix 3,3 dge.result (两个组,每个组3个重复,如2,,3,3为3个组分别有2/3/3个重复) $ ...
LPS_6h_3.isoforms.results \ Unstimulated.isoforms.results Unstimulated_2.isoforms.results \ Unstimulated_3.isoforms.results > IsoMat.txt ../software/RSEM-1.2.25/rsem-run-ebseq --ngvector mouse_ref.ngvec \ IsoMat.txt 3,3 IsoMat.results ../software/RSEM-1.2.25/rsem-control-fdr IsoMat.results...
rsem-run-ebseq --help to get usage information or visit thersem-run-ebseq documentation page. Second,rsem-control-fdrtakesrsem-run-ebseq's result and reports called differentially expressed genes/transcripts by controlling the false discovery rate. Run ...
ngvector.1.gz /usr/share/man/man1/rsem-gff3-to-gtf.1.gz /usr/share/man/man1/rsem-plot-transcript-wiggles.1.gz /usr/share/man/man1/rsem-prepare-reference.1.gz /usr/share/man/man1/rsem-run-ebseq.1.gz /usr/share/man/man1/rsem-simulate-reads.1.gz /usr/share/perl5/rsem_perl_...
> biocLite("edgeR") > biocLite("limma") > biocLite("DESeq2") > biocLite("ctc") > biocLite("Biobase") > install.packages("gplots") > install.packages("ape") $ /Analysis/DifferentialExpression/run_DE_analysis.pl --matrix genes.counts.matrix --method edgeR --samples_file samples_described...
~/software/rsem/rsem-run-ebseq \ GeneMat.txt2,2,2,2GeneMat.results #2,2,2,2表示4个condition,每个condition有两个重复;顺序要和3.1中输入文件表示的condition的顺序一致 #会得到三个文件 GeneMat.results.condmeans GeneMat.results GeneMat.results.pattern#GeneMat.results.pattern"C1""C2""C3""C4""...
LPS_6h_3.isoforms.results \ Unstimulated.isoforms.results Unstimulated_2.isoforms.results \ Unstimulated_3.isoforms.results > IsoMat.txt ../software/RSEM-1.2.25/rsem-run-ebseq --ngvector mouse_ref.ngvec \ IsoMat.txt 3,3 IsoMat.results ../software/RSEM-1.2.25/rsem-control-fdr IsoMat.results...
rsem-run-ebseq --help to get usage information or visit thersem-run-ebseq documentation page. Second,rsem-control-fdrtakesrsem-run-ebseq's result and reports called differentially expressed genes/transcripts by controlling the false discovery rate. Run ...