The problem about tophat software -G parameter

Question

[Wayne Lee]

Holle everyone! I am a beginner in RNA-Sequencing. I have a simple problem about 'tophat' software: what different on result between using -G parameter and do not use? If I use this parameter and give it a gene annotation file (e.g. gencode human V10) in reads alignment, can I use another version of annotation file (e.g. gencode human V19) when count reads number? Thank you very much!

[WouterDeCoster]

You should know that the old 'Tuxedo' pipeline of Tophat(2) 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. There are also other alternatives, including alignment with STAR and bbmap, or pseudo-alignment using salmon.

Please stop using Tophat https://t.co/Es4ohxOEyx Cole and I developed the method in *2008*. It was greatly improved in TopHat2 then HISAT & HISAT2. There is no reason to use it anymore. I have been saying this for years yet it has more citations this year than last #methodsmatter

— Lior Pachter (@lpachter) December 2, 2017

[ATpoint]

Not getting tired to enlighten the Tuxedo folks :-D

[WouterDeCoster]

Ya I should really write a bot to get this done.