Bowtie2 With Tophat?
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12.3 years ago
Caddymob ▴ 1000

Has anyone been able to run bowtie2 with tophat? Seems tophat is still reliant on Bowtie 0.12.7, but reading the specs on bowtie2 - it is probably a better option for >50bp reads.
bowtie rna • 4.0k views
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12.3 years ago
Caddymob ▴ 1000

Never mind.. I found it on seqanswers. Seems the answer is not yet..

Bowtie2 with Tophat
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Update. Now that tophat2 is available, you can use bowtie2 OR bowtie1.

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12.3 years ago

Not a direct answer to your question, but you might want to take a look at "Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM)":

http://www.ncbi.nlm.nih.gov/pubmed/21775302

Based on that paper, tophat would not be my first choice.
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I would have to agree with you.. RUM is a great solution, and so it RNASEQR...

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Just FYI, I have been tending to use gsnap.

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