I am analyzing Arabidopsis Rnaseq data. I was running Tophat and cufflinks, but after that I don't know which file of cufflinks I have to look for novel isoform. I used a reference annotation gtf file with cufflinks. I am analyzing Arabidopsis Rnaseq data . I was run tophat and cufflinks but after that i don't know which file of cufflinks i have to look for noval isoform . i used reference annotation gtf file with cufflinks.
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Question: How to find and extract novel transcript from cufflink and cuffdiff.
3.4 years ago by
rakeshsaraswat691 • 30
rakeshsaraswat691 • 30 wrote:
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3.3 years ago by
Jennifer Hillman Jackson ♦ 25k
Jennifer Hillman Jackson ♦ 25k wrote:
All isoforms will be present in the "transcripts.gtf" output from Cufflinks. Those without a known transcript name assigned from the reference annotation have novel splicing.
Best, Jen, Galaxy team
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