Thank you Devon for your reply. l want just to learn how can run cuffdiff correctly. I will have more biological replicates later. For this 2 current samples:
First, I used cuffmerge to merge the gtf files form cufflinks and then run cuffdiff. I got 71 sig genes.
In second run I just use cuffdiff with gtf annotation files and accepted_hits files (without gtf files from cufflinks) and got 412 sig genes.
the command that I used is:
cuffdiff \
-L A,B \
-o /home/cuffdiff \
/home/Homo_sapiens_UCSC_hg19/Homo_sapiens/UCSC/hg19/Annotation/Archives/archive-2014-06-02-13-47-56/Genes/genes.gtf \
/home/A/accepted_hits.bam /home/B/accepted_hits.bam
I would like to know which one is correct?
Thanks in advance
l want just to learn how can run cuffdiff correctly. I will have more biological replicates later. For this 2 current samples:
First, I used cuffmerge to merge the gtf files form cufflinks and then run cuffdiff. I got 71 sig genes.
In second run I just use cuffdiff with gtf annotation files and
accepted_hitsfiles (without gtf files from cufflinks) and got 412 sig genes.the command that I used is:
I would like to know which one is correct?
Thanks in advance
Both are correct, but the first result is probably more reliable, due to better matching the actual gene models used.