Question: Is blacklisted regions filtering in ChIP-seq still needed? (let's talk about the state of the art)
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gravatar for msimmer92
7 weeks ago by
msimmer92150
Uruguay
msimmer92150 wrote:

Hello, I am analysing ChIP-seq data and I saw the following post by @Devon Ryan (made 1 year, 7 months ago) https://bioinformatics.stackexchange.com/questions/458/when-to-account-for-the-blacklisted-genomic-regions-in-chip-seq-data-analyses/459#459?newreg=dca76bad61c443d7b4f0b1abd1487878 saying that, nowadays with the latest genome assemblies, one has less problems with blacklisted regions since they have been reduced.

I want to know, then, what's the state of the art of this situation? Should I remove them or not? (By the way, I was planning to use Deeptools to do it, but if it's not really necessary anymore I won't). Thank you!

filtering chip-seq blacklist • 195 views
ADD COMMENTlink modified 7 weeks ago by Devon Ryan88k • written 7 weeks ago by msimmer92150
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I would suggest to remove them. I am not sure if you have blacklisted for GRCh38, but if you are using GRCh37/hg19, you should remove them.

ADD REPLYlink written 7 weeks ago by geek_y9.3k
2

Link to blacklists. A simple bedtools intersect -v -a your_regions.bed -b blacklist.bed will do.

ADD REPLYlink written 7 weeks ago by ATpoint14k

@ATpoint do the bed files need to be sorted or something before doing that? thanks!

ADD REPLYlink written 7 weeks ago by msimmer92150
1

No, bedtools does not rely on sorted files.

ADD REPLYlink written 7 weeks ago by ATpoint14k
7
gravatar for Devon Ryan
7 weeks ago by
Devon Ryan88k
Freiburg, Germany
Devon Ryan88k wrote:

It's still considered best-practice to remove these regions. For genomes like GRCh38, the blacklisted regions are largely comprised of things like major satellite repeats, which are primarily located in hard-masked telomeric and pericentromeric regions. Given that, these regions will still show aberrantly high signal in all of your samples (thereby skewing normalization and often adding meaningless peaks).

ADD COMMENTlink written 7 weeks ago by Devon Ryan88k

Thank you for your fast reply! I will include it in my pipeline, then. Thank you also for the explanation about the location of repeats and therefore why is good to filter them anyways, even if you use the latest version of the assembly. (P.S: I didn't clarify but I'm working mostly with mouse and human genome). Follow-up question: you have any thoughts about if it is better to filter these regions with deepTools or with bedtools intersect (as another person commented here)?

ADD REPLYlink modified 7 weeks ago • written 7 weeks ago by msimmer92150
1

It doesn't much matter whether you filter with deepTools or bedtools intersect, you should get essentially the same results either way.

ADD REPLYlink written 7 weeks ago by Devon Ryan88k
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