Hi,

I have GTF files from spliceR which tell me which transcripts of certain genes are differentially expressed between different conditions. However, I am unable to find what the ids assigned to the transcripts (TCONS) correspond to. Is there a way to extract the transcript sequences corresponding to these ids using spliceR or any other tool?

Thank you!

Hi Aditi

SpliceR have not produced the transcripts - that was done by Cufflinks (judging from the TCONS abbreviation) so you need to go back and take the GTF file you used as imput to Cuffdiff.

Please note that it is not spliceR that does the differential expression - that is also Cufflinks/cuffdiff. spliceR is meant to analyze alternative splicing (not genes).

If you are interested in isoforms and isoform switches I will suggest you take a look at my new R package IsoformSwitchAnalyzeR instead.

Cheers

Kristoffer