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Old 04-13-2012, 01:34 PM   #1
elisadouzi
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Default Using bam file as the input for velvet

Has anyone tried to using bam file as the input for velvet? Can it automatically recognize the paired end information? I tried a little bit, seems velvet use it as single end reads.


Thanks!
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Old 04-13-2012, 04:27 PM   #2
swbarnes2
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Sure, it works fine. However, it will only recognize paired ends if the bam is sorted by read name, and not coordinate.

Picard can do this if your .bam is already sorted.
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