Question: need to identify CDS (translation) for gene models predicted by Cufflinks and Stringtie
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gravatar for Ann
3.2 years ago by
Ann2.2k
Concord NC USA
Ann2.2k wrote:

I have transcript models in GTF format made from assembling RNA-Seq read alignments using stringtie and also cufflinks. The reference genome is a new blueberry assembly I'm helping to annotate.

For the next steps, I need to find the genomic coordinates of the start and end of translation for the longest open reading in each transcript model.

Is there a program that can help me do that?

Previously, some-one in my group used a perl program called Tau to do this, but I don't have a copy of it. (Embarrassing!)

It seems like a straightforward task. Surely some-one has written something like this and put it on github or somewhere?

If not, do you think this would be a good project for a student learning bioinformatics?

 

 

 

 

rna-seq cufflinks stringtie • 1.1k views
ADD COMMENTlink modified 3.2 years ago by Chirag Nepal2.2k • written 3.2 years ago by Ann2.2k
0
gravatar for Chirag Nepal
3.2 years ago by
Chirag Nepal2.2k
Copenhagen
Chirag Nepal2.2k wrote:

You could try transdecoder

https://transdecoder.github.io/

 

ADD COMMENTlink written 3.2 years ago by Chirag Nepal2.2k
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