Mappability in duplicate gene?
0
0
Entering edit mode
5.9 years ago
Tania ▴ 180

Hi Every one

I am checking an interesting variant in a duplicate gene. I am checking mappability of the region, I get the Duke Unique_35 mappability from the UCSC genome browser. I took a window size greater than my read length and found the mappability is 1. Does this make sense given the gene is a duplicate? I thought if the gene is duplicate then it will have lower mappability? And is the window size reasonable? Am I missing anything here?

Thanks

exome sequencing variant calling • 1.1k views
ADD COMMENT
0
Entering edit mode

. I took a window size greater than my read length and found the mappability is 1.

how did you get that number ? cmd line ?

ADD REPLY
0
Entering edit mode

From IGV, I got the read length, say 150 and my variant is in the middle for example. then I checked the position of this gene by considering around 200 bases around my variant (I mean including the read length) in this window. I looked for Duke Unique_35 mappability in the UCSC. No command line.

Not sure if I explain it well.

ADD REPLY

Login before adding your answer.

Traffic: 1073 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