Question: Where to download blacklisted regions?
gravatar for saravanakumar992
2.3 years ago by
saravanakumar99220 wrote:

Where can one download the blacklisted regions from ucsc encode data? 

chip-seq blacklist • 3.1k views
ADD COMMENTlink modified 15 months ago by Ram14k • written 2.3 years ago by saravanakumar99220

Hello saravanakumar992!

We believe that this post does not fit the main topic of this site.

Not a real question nor tutorial

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.


ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by Michael Dondrup43k

Though quite poorly presented, this ends up being strongly related to ChIPseq analysis. I've rephrased it slightly so it's at least a bit more coherent (though still completely lacking in context) and reopened it.

ADD REPLYlink written 2.3 years ago by Devon Ryan78k
gravatar for Friederike
15 months ago by
United States
Friederike1.3k wrote:

just as an update for those in need of more recent blacklist regions (ce10, mm10, hg38), Anshul Kundaje supplies them here

ADD COMMENTlink written 15 months ago by Friederike1.3k

I have been working on these things lately. Here is some more information.

ADD REPLYlink written 15 months ago by venu5.0k

Hi @Friederike and @venu Why are hg38 and hg19 list different? EDIT: The hg38 list seems to be smaller probably because many regions have been fixed in hg38 assembly. Does the hg38 blacklist also contain mitochondrial homologs? I believe, the homologs remain whether it be hg19 or hg38. Any insights on this. Thanks!

ADD REPLYlink modified 7 months ago • written 7 months ago by abhishekniroula750

I have no deep insights into the specific differences between hg38 and hg19, but hg38 is generally considered to contain more "bait" sequences (meant to scavenge away reads that probably fell into some of the blacklisted regions before). I recommend to address Anshul Kundaje directly (and ideally share his response here).

ADD REPLYlink written 7 months ago by Friederike1.3k

It was reported have overlaps. I looked into the list and found the overlap: chr16 34586660 34587100 chr16 34587060 34587660

Some one have a updated or fixed one?



ADD REPLYlink written 16 days ago by weiyanjia20080

I'm afraid I don't understand the issue. Can you elaborate?

ADD REPLYlink written 12 days ago by Friederike1.3k

When I use this file as a blacklist to run deeptools-bamcompare, it was reported this list has overlaps. chr16 34586660 34587100 chr16 34587060 34587660

My understand is the bottom range overlaps with the top one. 34587060 < 34587100

ADD REPLYlink written 12 days ago by weiyanjia20080

you could use bedtools merge -i blacklist.bed to merge those overlapping regions.

ADD REPLYlink written 7 days ago by Friederike1.3k
gravatar for Devon Ryan
2.3 years ago by
Devon Ryan78k
Freiburg, Germany
Devon Ryan78k wrote:

There's not yet a blacklist available for each species or even each version of mouse/human. You can get the mm9 blacklist here. The equivalent for hg19 is here. There's no equivalent for hg38 and I'm not sure that lifting things over will work, though you could certainly try. We have an mm10 version of this, but I don't know that it's publicly available.

ADD COMMENTlink written 2.3 years ago by Devon Ryan78k
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