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What read aligner are you using for RNAseq?

Brett Hayes
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What read aligner are you using for RNAseq? Oval 17

I've considered using tophat2, but not sure which one is widely used these days.. :thinking_face:

Thanks!

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Posted: 7 months ago
Roy Winters
Research Fellow at University of Melbourne
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Roy Winters

Research Fellow at University of Melbourne

@brett.hayes81:u note that tophat is considered to be outdated.. (they even state so in their website) so you should try @hisat2 instead

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Posted: 7 months ago
T Bradley
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@brett.hayes81:u @Roy.Wormi:u Definitely don't waste your time on tophat I'm working with the STAR aligner which is super fast and gives me great results. You can select if you wish to align to the genome and also transcriptome

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Posted: 7 months ago
Brett Hayes
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@Roy.Wormi:u @Tim.Bradley:u Thanks for your suggestions! I've selected to use STAR (I found it's also the selected aligner used by 10X genomics, so it must be good). I found it very fast and easy to use.. but not sure how can one appreciate the output

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Posted: 6 months ago