Question: How to find novel gene/isoform in 1 RNA-SEQ sample?
gravatar for Whoknows
3.3 years ago by
Whoknows830 wrote:


I have only one human RNA-SEQ sample and I wanted to find novel isoforms and also novel genes from this sample.

I have performed Topaht2 and Cufflinks, which cufflinks generates 4 files for me.

Should I run Cuffcompare to find novel isoforms / genes? or I should use cufflinks output files?


rna-seq next-gen • 1.6k views
ADD COMMENTlink modified 3.3 years ago by EagleEye6.7k • written 3.3 years ago by Whoknows830

You should know that the old 'Tuxedo' pipeline of Tophat and Cufflinks is no longer the "advisable" tool for RNA-seq analysis. The software is deprecated/ in low maintenance 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.) There are also other alternatives, including alignment with STAR and bbmap, or pseudo-alignment using kallisto or salmon.

ADD REPLYlink written 3.3 years ago by WouterDeCoster44k

thanks, I have read that 2016 paper but I cannot find relevant information about how to find novel isoforms by HISAT. I just want to quantify expression of novel isoforms.

ADD REPLYlink written 3.3 years ago by Whoknows830
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1183 users visited in the last hour