Mappability in duplicate gene?

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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 • link 5.9 years ago by Tania ▴ 180

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. 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 • link 5.9 years ago by Pierre Lindenbaum 161k

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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 • link 5.9 years ago by Tania ▴ 180

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