Question: cuffcompare and cuffmerge
0
gravatar for qudrat
9 weeks ago by
qudrat30
NATIONAL INSTITUTE OF IMMUNOLOGY, INDIA
qudrat30 wrote:

Hi folks, To find novel transcript in an organism via RNA-Seq, some use Cuffcompare to merge different gtf files produced from Cufflinks while some use Cuffmerge for the same. Please help me to get over this. Thank you

rna-seq next-gen • 147 views
ADD COMMENTlink written 9 weeks ago by qudrat30
2

I believe (but might be wrong) that you have been told before that the pipeline tophat-cufflinks-cuffmerge is no longer the accepted best pipeline for RNA-seq analysis and should be replaced by HISAT2, StringTie and ballgown. See this paper: Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. (If you can't get access to that publication, let me know and I'll -cough- help you.)

ADD REPLYlink written 9 weeks ago by WouterDeCoster24k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1311 users visited in the last hour