rna seq analysis

Question

[anitha.b]

Hi, I have gencode long non coding(lnc) gtf and lnc reference fasta files.. if i run tophat using these two references, i am getting an error "gtf_to_fasta returned an error". how to solve this??? any suggestions please.

Thank you Anitha

[WouterDeCoster]

Unless you have good reasons to do otherwise you should be aligning to the full genome, and not just to your "lnc reference fasta files".

Note: Tophat-Cufflinks is no longer the recommended RNA-seq processing pipeline. A new protocol is described here: Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown, but there are many more alternatives.

Finally: Please choose a more informative title for your thread.

Answer 1

[Bruce]

I am doing the same things,how about now?