Tophat alignment against BALB_cJ_R

Question

[anu014]

Greetings of the day Biostars!

Can anyone tell me where can I download genome for BALB_cJ_R ? I'm trying to align it with TopHat. All I know about it is this link: http://mice-geval.sanger.ac.uk/BALB_cJ_R20150812/Info/Index

Please help me. Thank you :)

[WouterDeCoster]

Since it seems you are starting out on a new project 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 salmon.

Answer 1

[Devon Ryan]

You can download that here. Do not use Tophat2!