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Question: How to find and extract novel transcript from cufflink and cuffdiff.
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gravatar for rakeshsaraswat691
3.4 years ago by
rakeshsaraswat691 • 30
India
rakeshsaraswat691 • 30 wrote:

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. 
galaxy • 2.3k views
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modified 3.3 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.4 years ago by rakeshsaraswat691 • 30
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gravatar for Jennifer Hillman Jackson
3.3 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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
ADD COMMENT • link written 3.3 years ago by Jennifer Hillman Jackson ♦ 25k

I have two condition with 3 replicate each, gives me 3 transcript.gtf files for each condition. How i merge these transcripts.

ADD REPLY • link written 3.3 years ago by rakeshsaraswat691 • 30
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