#8 Mapping software

[Anonymous]

Originally created by: mr.gauth... (code.google.com)@gmail.com

Hi,

I try to use Popoolation with .sam from Bowtie2 and not BWA, because Bowtie2 parameters interest me, but I obtain only "na" in the final output.

Despite many tests I don't find solution and I don't know which step is problematic...

Do you have any ideas?

Thanks

Jeremy

[Anonymous]

Originally posted by: RoKof... (code.google.com)@gmail.com

it should not make a difference whether you use bwa or bowtie,
as long as you obtain a valid pileup file.
maybe the quality encoding?
did you make sure that you used the right quality encoding?