chapmanb/cloudbiolinux — comment on commit 77b8cc5bee00e8600b1f08a451789e4cdf9e934c
File:  line 0
By chapmanb:

Roman -- ugh, is it a reproducible problem that you could bring up to the TopHat developers? I've done TopHat on standard mm9 without any problems, so it must be something with the dataset. The thing I'd worry about with masked genomes is missing the "real" best hit for a read due to it being masked, and instead mapping to a less good hit within the error threshold.

Pjotr -- we normally get folks who want a representation of repeat regions (typically, sample 1 position randomly) as well and it's nice not to have to keep two indexed versions around.