How to obtain low mappability regions from UCSC for deepTools computeGCBias?
Entering edit mode
11 months ago
chiefcat ▴ 180


Does anyone know how to download low mappability regions from UCSC for computeGCBias?

In deepTools documentation, it said, "You can download the mappability tracks for different read lengths from UCSC, e.g. for mouse and human."

When I go to UCSC, there are different files, which one should I use?

Or alternatively, can I just use the blacklists from ENCODE and modENCODE consortia instead?

Thanks! Chiefcat

deepTools • 799 views
Entering edit mode

There are a couple of answers about how to make these files in a prior thread. See if that is useful: Where can I get ?or how can I make a mappability track for hg38 assembly

Entering edit mode
11 months ago
rfran010 ▴ 900

I personally didn't find mappability tracks for mm10 either, but there are some for mm9.

I would note that there is a major difference in blacklist regions and mappability tracks. I understand blacklist regions are for regions that can be artifacts with very high signal, while mappability focuses more on uniqueness of sequences. Also, I don't think blacklists have values associated with their regions, while mappability tracks will.

For deeptools, I think it mainly ignores the mappability value and tries to just exclude regions of low mappability (i.e. excludes regions of low signal, while blacklists exclude regions of high signal). In my experience the majority of these regions are the repetitive regions, so a better alternative than using blacklists may be using a repeatMasker track/table.


Login before adding your answer.

Traffic: 1412 users visited in the last hour
Help About
Access RSS

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

Powered by the version 2.3.6