The problem about tophat software -G parameter
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!
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Wayne Lee •
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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.
Not getting tired to enlighten the Tuxedo folks :-D
Ya I should really write a bot to get this done.