Aligner For Mapping Mate Pair (Outies) Data

Question

[Abhi]

Hi All

I have a mate paired reads (facing outwards) with highly variable insert size. Any aligner that will allow me to map these reads as well as pair them up.

Also I should mention the length of read 1/2 in my case are not equal due to linker cleaning step which will remove linker sequence from the read and it can be found at any random position in the read.

Best, -Abhi

Answer 1

[Chris Whelan]

I've had decent luck with Novoalign for mate pair data. The mate pair data sets I've worked with have had significant contamination by paired-end reads (innies) and Novoalign has built in logic to deal with those pairs:

http://www.novocraft.com/wiki/tiki-index.php?page=Paired+Read+Modes

I haven't personally used Stampy but I hear that it can also work well.

Answer 2

[SES]

You did not say what kind of data you have. NovoAlign, Stampy, and I believe MAQ will all do the job. You will want to select the right tool for your data though.

[Abhi]

@SES : data is for cDNA but the read length after trimming is < 80 bp which is significantly smaller than the exon size. I dont see an issue as most of the reads should map within an exon and only a small chunk should come from exon-exon boundaries.