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Old 04-13-2012, 01:34 PM   #1
Location: US

Join Date: Mar 2011
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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.

elisadouzi is offline   Reply With Quote
Old 04-13-2012, 04:27 PM   #2
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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.
swbarnes2 is offline   Reply With Quote

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