Paired End Mapping : What Is Bwa Solid Paired End Default Direction (Bwa Sampe) ?

Question

[Hx]

Hi,

SOLiDTM Library construct

For Paired End

F3 F5

---------><----------

Can anyone tell me the default directions on how BWA will map paired ends?

Thanks in advance.

Answer 1

[brentp]

BWA expects mate-pair F3/R3 (as input to solid2fastq.pl).

You could reverse-complement your F5 reads (and reverse the quality) and send them to solid2fastq.pl and it should work more/less as expected. Then you just have to consider how having the low-quality bases at the start of the read affects BWA (lh3?) -- you may want to quality trim your reads before-hand.

EDIT: if this works, it would be just reverse, not reverse-complement of the F5 reads.

[Hx]

Thanks brentp, solve my question mark on weird flagstats. However, regarding "reverse-complement your F5 reads (and reverse the quality)" as you mentioned, can I know how to reverse the reads?

[brentp]

just reverse complement the reads. You can do this with bioperl or biopython. In perl, it's like my $rc = reverse(seq); =~ tr/ACGTacgt/TGCAtgca/. So just loop over the csfasta and do that to every other line. And for the qual file. Just reverse it.

[Hx]

SOLiD reads are colourspace reads where I cant perform reverse complement on them, are there any other ways?

[brentp]

Oh, yes of course. I think in colorspace, you can just reverse the colorspace sequence, without complementing to get (what would be in base-space) the reverse complement. I havent mapped F3/F5 Solid reads but maybe check the -c parameter to bwa (http://bio-bwa.sourceforge.net/bwa.shtml)

[Hx]

I'm not sure whether this works, will give a try, thanks for the suggestions brentp, but I'm still hoping for a more concrete solution, perhaps other software may help

Answer 2

[Yaira04]

Hi HX,

did you find any better solution eventually? I am confronting the same issue these days...

Thanks.

[Hx]

Yaira, it seems there's no concrete solution for bwa paired end mapping yet since bwa assumes paired end mapping has the same orientation as mate pair, maybe you can consider trying out Bioscope or try using bfast http://seqanswers.com/forums/showthread.php?t=7100 or bowtie http://bowtie-bio.sourceforge.net/manual.shtml#paired-end-colorspace-alignment