Keeping loci those have specific number of SNPS
0
1
Entering edit mode
12 months ago
safiq713 ▴ 10

Dear all

I want to keep some loci, only those loci has 4 SNPS (specific number of SNPS). I want to make skyline plot from ddRAD data. Do you have any idea how can go forward

Thanks a lot for your help

SkylinePlot • 251 views
ADD COMMENT
0
Entering edit mode

may be you can create sliding windows and count SNPs within them and keep the ones that has more than 'n' SNPs. and then merge overlapping windows post-hoc to have a consensus loci. This can be achieved by bedtools and a bit of scripting. I am not aware of any tools that does this.

ADD REPLY

Login before adding your answer.

Traffic: 1766 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