How to find novel gene/isoform in 1 RNA-SEQ sample?

Question

[Whoknows]

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

[WouterDeCoster]

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.

[Whoknows]

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.

Answer 1

[EagleEye]

Checkout these posts

how many replicates are required for discovery of novel isoform using RNA-seq and cufflinks RABT assembly

A: What is best tool to call diferentially expressed isforms ?

A: workflow/tool for alternative splicing

C: What is the best tool for isoform function prediction?