Hi all,
I'm running through the cufflinks-cuffcompare-cuffdiff pipeline using three samples, but for some reason cuffdiff is only producing one of each kind of differential expression file (*_exp.diff) rather than one for each pair of samples. In the *.fpkm_tracking files, all 3 samples are showing up (q1,q2,q3) but I'm only getting expression files comparing q1 and q2. Any ideas?? Here's the basics of the cuffdiff command I'm using:
cuffdiff -q -r ref.fa cuffcompare_6hr.4/stdout.combined.gtf tophat_out_1/sample1.bam tophat_out_2/sample2.bam tophat_out_3/sample3.bam
Anyone else running cuffdiff on >2 samples using the latest version?
Thanks!
I'm running through the cufflinks-cuffcompare-cuffdiff pipeline using three samples, but for some reason cuffdiff is only producing one of each kind of differential expression file (*_exp.diff) rather than one for each pair of samples. In the *.fpkm_tracking files, all 3 samples are showing up (q1,q2,q3) but I'm only getting expression files comparing q1 and q2. Any ideas?? Here's the basics of the cuffdiff command I'm using:
cuffdiff -q -r ref.fa cuffcompare_6hr.4/stdout.combined.gtf tophat_out_1/sample1.bam tophat_out_2/sample2.bam tophat_out_3/sample3.bam
Anyone else running cuffdiff on >2 samples using the latest version?
Thanks!
Comment