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Old 09-24-2009, 09:22 AM   #182
apfejes
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Location: Oakland, California

Join Date: Feb 2008
Posts: 236
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I seem to recall that bowtie is able to produce .map files - which would be pre-sorted and directly readable by FindPeaks without breaking it up into chromosomes. That might be a good first pass to try. (Assuming this is SET data. if it's PET data, you'll need to do the pairing anyhow, so SeparateReads wouldn't have been the right path to take.)

I suppose I should also mention that running SortReads.jar on .gz bowtie files *should* work. If you could send me the error you're getting, I may be able to track down the reason why it's not working for you.

And finally, I should probably also mention that bowtie seems to be doing something funny to your chromosome names. I don't use bowtie myself, but someone had previously reported to me that there was an option you can use to get more "sane" chromosome names. I would suggest you take a look - it may help you out downstream.
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