Aligner For Mapping Mate Pair (Outies) Data
2
0
Entering edit mode
12.6 years ago
Abhi ★ 1.6k

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 • 3.9k views
ADD COMMENT
1
Entering edit mode
12.5 years ago
Chris Whelan ▴ 570

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.

ADD COMMENT
0
Entering edit mode
12.6 years ago
SES 8.6k

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 COMMENT
0
Entering edit mode

@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 REPLY

Login before adding your answer.

Traffic: 970 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6