Question: How to find novel gene/isoform in 1 RNA-SEQ sample?
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gravatar for Whoknows
2.7 years ago by
Whoknows760
Tehran,Iran
Whoknows760 wrote:

Hello

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?

Thanks

rna-seq next-gen • 1.4k views
ADD COMMENTlink modified 2.7 years ago by EagleEye6.5k • written 2.7 years ago by Whoknows760

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 2.7 years ago by WouterDeCoster42k

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 2.7 years ago by Whoknows760
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