Cuffdiff outputs no significant AS genes in RNA-seq analysis.
Hi All
I did my first RNA-seq analysis on A.thaliana dataset using Tophat, Cufflinks, Cuffmerge and Cuffdiff at Iplant's DE. As a beginner, I used the default settings and supplied the reference annotation and sequence downloaded from Tophat's site.
However, Cuffdiff produces no significant alternatively spliced genes. Is it common to get no significant AS genes when comparing two samples at different temperatures with no replicated?
The DE genes as output by cuffdiff doesn't match any but one gene from the those reported by a publication whose data I've used. They din't use Tophat and Cufflinks for their analysis though. How common is it to get completely different results using different pipelines?
I did my first RNA-seq analysis on A.thaliana dataset using Tophat, Cufflinks, Cuffmerge and Cuffdiff at Iplant's DE. As a beginner, I used the default settings and supplied the reference annotation and sequence downloaded from Tophat's site.
However, Cuffdiff produces no significant alternatively spliced genes. Is it common to get no significant AS genes when comparing two samples at different temperatures with no replicated?
The DE genes as output by cuffdiff doesn't match any but one gene from the those reported by a publication whose data I've used. They din't use Tophat and Cufflinks for their analysis though. How common is it to get completely different results using different pipelines?