Question: Aligner For Mapping Mate Pair (Outies) Data
gravatar for Abhi
8.6 years ago by
United States
Abhi1.5k wrote:

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

alignment next-gen sequencing • 2.9k views
ADD COMMENTlink modified 8.6 years ago by Chris Whelan550 • written 8.6 years ago by Abhi1.5k
gravatar for Chris Whelan
8.6 years ago by
Chris Whelan550
Portland, OR
Chris Whelan550 wrote:

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:

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

ADD COMMENTlink modified 13 months ago by RamRS30k • written 8.6 years ago by Chris Whelan550
gravatar for SES
8.6 years ago by
Vancouver, BC
SES8.4k wrote:

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.

ADD COMMENTlink written 8.6 years ago by SES8.4k

@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.

ADD REPLYlink written 8.6 years ago by Abhi1.5k
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