How do I generate the correct input files for Blast2GO from CuffLinks2 output?

Question

[ryan.c.gott]

Hi everyone,

Sorry if this is a "no-brainer" type of question, I just started assembling my first transcriptome last week (and am having a really good time learning how to work with all these data!). I couldn't find anything to quite answer my questions while searching previous questions.

I'm currently working with a simple exploratory transcriptome, just two biological replicates of the same treatment, so there is no differential expression analysis that I will be doing. I've just finished my alignment using TopHat2 and my assembly using CuffLinks2 and would now like to get my GO terms using Blast2GO. I know Blast2GO needs .fasta files in order to run blast, but I do not know how to generate these .fasta files given the CuffLinks2 output files (or do I use something from TopHat2?). Is there any way to do this? Or is there a different option I need to include before actually running the assembly in order to get the correct file formats from CuffLinks2? Thanks for your advice!

Answer 1

[Istvan Albert]

Cuffdiff produces a file calledtranscripts.gtf this contains the coordinates for the transcripts, cufflinks also comes with a tool called gffread that can be used with the reference genome and the transcripts.gtf file to produce a fasta file with the transcripts.