Question: The problem about tophat software -G parameter
gravatar for Wayne Lee
2.0 years ago by
Wayne Lee10
Wayne Lee10 wrote:

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!

rna-seq alignment tophat • 532 views
ADD COMMENTlink written 2.0 years ago by Wayne Lee10

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.

ADD REPLYlink written 2.0 years ago by WouterDeCoster43k

Not getting tired to enlighten the Tuxedo folks :-D

ADD REPLYlink written 24 months ago by ATpoint32k

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

ADD REPLYlink written 24 months ago by WouterDeCoster43k
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