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Old 07-09-2010, 12:57 PM   #4
Location: Ithaca, NY

Join Date: Apr 2010
Posts: 39

Ah yes, didn't think about that, either.. I'm in the same boat, I've been hosting on my own network. One thing that helps me is filtering out unmatched reads, even if only for viewing on UCSC. I aligned to chromosomes in a genome, so all of my references were chr*. To filter, I did grep chr file.sam > file.noun.sam, then generated bam files from there.
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