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Old 10-17-2012, 01:10 PM   #6
IBseq
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Location: uk

Join Date: Jul 2012
Posts: 56
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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,
ib
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