I'm working on RNA-Seq data. Here's my basic workflow :
STAR -> cufflinks -> cuffmerge
So after that, I've a merged transcriptome gtf file. Now I want to annotate it to furthyer use it in differential expression analysis. So here's my idea. First extract the transcritp sequence using the gtf coordinates. Then, blast each sequence against ensembl transcript to annotate them.
What do you think ? Is there maybe another tool ?