Software for variable-length PE reads

[shazzle]

Hi guys,

I have variable length PE reads from taking out adapters in Illumina data.

I have run these reads on bwa using the sampe option. However I always end up with "bwa Potential bug: (125,125) > 123" (and waited for 6 hours before finally giving up. I ran it twice by rebuilding the SA just to make sure). Previous commands before reaching this stage all worked fine. This is aligned to hg18.

I have since tried to find other aligners that can do variable length PE. Any suggestions?

[Torst]

I have variable length PE reads from taking out adapters in Illumina data.
I have run these reads on bwa using the sampe option. However I always end up with "bwa Potential bug: (125,125) > 123" (and waited for 6 hours before finally giving up. I ran it twice by rebuilding the SA just to make sure). Previous commands before reaching this stage all worked fine. This is aligned to hg18.

How do you know the variable length is the issue - does the bug occur when you give BWA the un-trimmed reads?