Question: rna seq analysis
gravatar for anitha.b
3.2 years ago by
anitha.b0 wrote:

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

rna-seq • 710 views
ADD COMMENTlink modified 2.8 years ago by Bruce0 • written 3.2 years ago by anitha.b0

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.

ADD REPLYlink modified 3.2 years ago • written 3.2 years ago by WouterDeCoster43k
gravatar for Bruce
2.8 years ago by
Bruce0 wrote:

I am doing the same things,how about now?

ADD COMMENTlink written 2.8 years ago by Bruce0
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