Using bam file as the input for velvet

[elisadouzi]

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!

[swbarnes2]

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.