blacklisted chip regions

[James Saliba]

Hello,

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 show aberrantly high signal in all of the samples (thereby skewing normalization and often adding meaningless peaks).

ENCODE has generated a bd file of all of them hg38.blacklist.bed.gz

it is good practice to remove them. i thaught the pipeline did however, lots of my peaks are being called from them.

online it says a command like this removes them:

bedtools intersect -v -a your_regions.bed -b blacklist.bed

however i am not an expert coder and dont know how to split the pipeline in half to be able to do so when my bed files are made and then resume.

what line can i add to the generated pipeline script and where?

or how can i fix the issue

Thanks

[Mareike Janiak]

Hi James, 

Thanks for bringing this to our attention. 

We agree that this would be a useful step to add to the pipeline, so if you can wait a little bit, we can work on implementing this for one of the next releases. 

Let me know if that works for you. 

Best, 

Mareike

[James Saliba]

Sounds great thanks!