Tophat alignment against BALB_cJ_R
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 :)
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Devon Ryan
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anu014
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anu014
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You can download that here. Do not use Tophat2!
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Devon Ryan
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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.