How can I find the official gene ID correspond to the CUFF ID in cufflinks output

Question

[hana]

I run cufflinks with out annotation reference genome (gtf file) to find the novel transcripts. How can I find the official gene ID correspond to the CUFF ID in cufflinks output?

thank you

[Devon Ryan]

Why don't you just use the reference annotation and also look for novel transcripts (see the -g option)? That would seem vastly simpler.

[hana]

Thanks all for your reply

I have used the cufflinks with -g option , and got a lot of genes with CUFF ID. Can anybody explain it for me.

Thank you

[Devon Ryan]

Those should be novel isoforms.

[hana]

thank you so much

[charbel.feghaly]

hello hana ,

i am facing the same issue, so what did you do with those CUFF ID to observe the novel trancripts ?

[jiskroyer]

I'm also curious what I should do with them (the CUFF IDs). For the record, I used the -g option and ran cufflinks but not cuffdiff.

Answer 1

[super]

The cufflinks and cuffdiff use annotation reference genome (gtf file) . However, you could also use Biomart to find the official Gene symbol, Gene ID or Ensembl ID, and transfer among them.

Answer 2

[Mikael Huss]

Using cuffcompare with a GTF file containing "official" IDs should be the quickest way. It gives you "class codes" that tell you which transcripts that match annotated genes wholly or partially and which are novel relative to the annotation.