Question: Blacklisted regions for mm10
0
gravatar for rbronste
23 months ago by
rbronste230
rbronste230 wrote:

Hi,

Trying to find out where I can get the most recent file of mm10 blacklisted regions? Thank you.

Rob.

chip-seq blacklisted regions • 1.6k views
ADD COMMENTlink modified 23 months ago by Santosh Anand4.6k • written 23 months ago by rbronste230

What is the definition of blacklisted regions?

ADD REPLYlink modified 23 months ago • written 23 months ago by Santosh Anand4.6k

"regions in the human genome that have anomalous, unstructured, high signal/read counts in next gen sequencing experiments independent of cell line and type of experiment."

I have this info for mm9 which I guess I can liftover but was wondering if there were any updated BED files.

Thanks

ADD REPLYlink written 23 months ago by rbronste230

Just curious: where you got this info from (url)? Lift over is a good idea indeed (and may be the only possibility!)

ADD REPLYlink written 23 months ago by Santosh Anand4.6k

Lifting over blacklisted regions generally doesn't work, since it's typically the case that those regions have been resolved in subsequent releases.

ADD REPLYlink written 23 months ago by Devon Ryan88k

Hi Devon, as I understand, the blacklisted regions refers to NextGen experiments, not to the Genome assembly per se. A new genome assembly might resolve the regions not assembled earlier. But these regions are not always the same regions which will have anomalous read counts in Next-Gen experiments. These two seem to be different things to me.

ADD REPLYlink written 23 months ago by Santosh Anand4.6k

They're often one and the same. The regions tend to overlap assembly issues. Yes, this won't always be the case, but this is much of the reason for the difference in blacklisted regions between GRCh38 and GRCh37.

ADD REPLYlink written 23 months ago by Devon Ryan88k

I'm getting more confused, sorry :) If the regions are not in the genome assembly in the very first place, how can NGS reads map there? For me, it seems like the blacklisted regions are mostly repeats, which are present in the assembly, but it is difficult to map NGS reads on them. In this sense, they are "resolved" in assembly, but difficult to map NGS reads on them.

ADD REPLYlink written 23 months ago by Santosh Anand4.6k

Often the copy number in the assembly has been fixed. For repeats, this makes the resulting alignments actually repetitive in the newer assembly so there's no reason to blacklist since you no longer get aberrant peaks.

ADD REPLYlink written 23 months ago by Devon Ryan88k
1
gravatar for James Ashmore
23 months ago by
James Ashmore2.6k
UK/Edinburgh/MRC Centre for Regenerative Medicine
James Ashmore2.6k wrote:

Select mm10 in the drop-down box

https://www.encodeproject.org/annotations/ENCSR636HFF/

ADD COMMENTlink written 23 months ago by James Ashmore2.6k
1
gravatar for YaGalbi
23 months ago by
YaGalbi1.4k
Biocomputing, MRC Harwell Institute, Oxford, UK
YaGalbi1.4k wrote:

The ATAC-seq authors recently created a mitochondrial blacklist (found here) for use on ATAC-seq data which represents high signal regions on the nuclear genome caused by read sequence homology with the mitochondrial genome. A signal artifact blackist has also been created by ENCODE (found here).

In the command line:

for i in *.bedfile; do bedtools intersect -v -a $i -b [PATH]/mitochondrial.blacklist.bed [PATH]/signal.artifact.blacklist.bed > $i.bed; done

Be careful to not create an infinite loop with this command (all the files may end in .bed)

ADD COMMENTlink modified 23 months ago • written 23 months ago by YaGalbi1.4k
1
gravatar for Santosh Anand
23 months ago by
Santosh Anand4.6k
Santosh Anand4.6k wrote:

Probably you are looking for this

https://sites.google.com/site/anshulkundaje/projects/blacklists

ADD COMMENTlink written 23 months ago by Santosh Anand4.6k
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