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Old 02-11-2013, 04:30 PM   #2
Senior Member
Location: San Diego

Join Date: May 2008
Posts: 912

Sounds like downsampling would make your life easier.

Removing duplicates would be one quick way of accomplishing this. But there are other ways. Picard, for one, can downsample a .bam. You can also do a quick and dirty version yourself, by grepping for reads, say, from one tile.
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