View Single Post
Old 10-17-2012, 01:10 PM   #6
Location: uk

Join Date: Jul 2012
Posts: 56

hi robby, not sure if you sorted out but I write it anyway...

"Maybe I do something wrong. I did the following:
1. cufflinks -G ucsc-reference.gtf sample_n.bam (for all samples)
2. cuffdiff ucsc-reference.gtf sample_1.bam sample_2.bam [....] sample_n.bam
3. compare genes.expr (cufflinks) with genes.fpkm_tracking (cuffdiff)

you run cufflinks correctly, but then you need to run cuffcompare and then use the output of cuffcompare to run cuffdiff to which you will provide as well the sam/.bam files from tophat...

hope it helps,
IBseq is offline   Reply With Quote