Wednesday 27 October 2010

Tophat adds support for strand-specific RNA-Seq alignment and colorspace

Hooray!
testing Tophat 1.1.2 now
1.1.1

on a 8 Gb Ram CentOS box managed to align 1 million reads to hg18 in 33 mins and 2 million reads in 59 mins. using 4 threads
Nice scalability! But it was slower than I was used to for bowtie. I kept killing my full set of 90 million reads thinking there's something wrong. Guess I need to be more patient and wait for 45 hours.

I do wonder if the process can be mapped to separate nodes to speed up.

3 comments:

  1. Does Myrna support colorspace yet? I wonder how long it takes changes in Tophat to ripple through to there.

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  3. I am wondering when will colorspace for Tophat be supported in Galaxy as well.

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Datanami, Woe be me