Question: How to find and extract novel transcript from cufflink and cuffdiff.
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gravatar for rakeshsaraswat691
3.1 years ago by
India
rakeshsaraswat69130 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 • 2.1k views
ADD COMMENTlink modified 3.0 years ago by Jennifer Hillman Jackson25k • written 3.1 years ago by rakeshsaraswat69130
0
gravatar for Jennifer Hillman Jackson
3.0 years ago by
United States
Jennifer Hillman Jackson25k 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 COMMENTlink written 3.0 years ago by Jennifer Hillman Jackson25k

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

ADD REPLYlink written 3.0 years ago by rakeshsaraswat69130
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