Wednesday, 27 October 2010

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

testing Tophat 1.1.2 now

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.


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

  2. This comment has been removed by the author.

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


Datanami, Woe be me