Question: rna seq analysis
0
gravatar for anitha.b
2.2 years ago by
anitha.b0
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 • 569 views
ADD COMMENTlink modified 21 months ago by Bruce0 • written 2.2 years ago by anitha.b0
2

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 2.2 years ago • written 2.2 years ago by WouterDeCoster39k
0
gravatar for Bruce
21 months ago by
Bruce0
CHN
Bruce0 wrote:

I am doing the same things,how about now?

ADD COMMENTlink written 21 months ago by Bruce0
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