Appropriate k-mer size for mappability mask
0
0
Entering edit mode
2.5 years ago

As part of MSMC, you need a mappability mask. However, for non-model organisms, you'll likely have to generate the masks yourself. I am using 3 spined sticklebacks, and my sequencing for each individual is comprised of 3 different libraries; 100bp reads with 140bp and 300bp insert sizes, and 50bp reads with 3kb insert sizes.

The program SNPable is conceptualised with single-end reads in mind, so deciding on which size k-mer to use is difficult. A guide I read used 250-mers for a single paired end library, though they didn't state the size of the reads nor the insert.

My question is simple, what do I need to consider when deciding what size k-mer to use? The mate pair library makes this particularly difficult, or so I have been led to believe at least. Any help would be greatly appreciated.

SNPable Mappability • 858 views
ADD COMMENT

Login before adding your answer.

Traffic: 2551 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