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ENCODE-DCC / chip-seq-pipeline2

ENCODE ChIP-seq pipeline
MIT License
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Deactivated link. #161

Closed abearab closed 4 years ago

abearab commented 4 years ago

This page where you said

Get a URL for a gzipped blacklist BED file for your genome. If you don't have one then skip this step. An example blacklist for hg38 is here.

the link is not working.

leepc12 commented 4 years ago

It's here. https://storage.googleapis.com/encode-pipeline-genome-data/hg38/hg38.blacklist.bed.gz

akundaje commented 4 years ago

@leepc12 is this updated to the latest blacklist

leepc12 commented 4 years ago

@akundaje: No, it's an old one. New blacklist is here. https://www.encodeproject.org/files/ENCFF356LFX/@@download/ENCFF356LFX.bed.gz

akundaje commented 4 years ago

Ok. We should update the default pipeline blacklist for GRCh38 to the latest one

On Mon, Jun 15, 2020, 8:50 AM Jin Lee notifications@github.com wrote:

@akundaje https://github.com/akundaje: No, it's an old one. New blacklist is here.

https://www.encodeproject.org/files/ENCFF356LFX/@@download/ENCFF356LFX.bed.gz

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leepc12 commented 4 years ago

Sure, will update ref genome TSV files with accessioned files (including the latest blacklist uploaded to the portal) only in the next release.

leepc12 commented 4 years ago

Fixed in the latest release. Closing this.