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

Hello,
My problem is actually with mapping against the repeat masked mm9 genome. I've indexed it with bowtie-build and am trying tophat on it. However, i get a "Error: Report generation failed with err = 1". I've poked around for this and it seems to be an I/O error but i have no idea where it could stem from.
Furthermore, the reason i'm even considering the rm version is because of some "interesting" tophat behavior. It would seem to get biased towards the repeats and completely miss good non-repeat mapping. I know this sounds very strange, but i have a couple of reads (picked 5 by hand) that it maps nicely if i run them by themselves. However, when they are in a big library with a lot of "junk-repeats" it completely misses them.