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update Blacklists used in the pipelines #228

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sopenaml opened this issue Oct 13, 2021 · 2 comments
Closed

update Blacklists used in the pipelines #228

sopenaml opened this issue Oct 13, 2021 · 2 comments
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@sopenaml
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sopenaml commented Oct 13, 2021

The blacklists used by the pipeline seem to be an old version, with fewer entries than the ones we can find in the newly updated versions here: https://sites.google.com/site/anshulkundaje/projects/blacklists

For instance, the GRcm38 provided with the 1.2.2 chipseq version appears to have 164 entries, while the mm10 one in the followig link https://github.com/Boyle-Lab/Blacklist/tree/master/lists (version 2) has 3435 entries.
For human there's even a newer update version3, it would be great if the most up to date versions would be provided with the pipelines
Would it be possible to update them please? @jose Espinosa-Carrasco

@JoseEspinosa
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JoseEspinosa commented Jan 26, 2022

Thanks for reporting @sopenaml ! We are working on the transition to DSL2 and we should also include the updated blacklists. Anyway, if you want to provide the updated blacklist bed with the current stable version of the pipeline, you could use the blacklist parameter to the nextflow command you use e.g. "--blacklist /path/to/your/updated/file/mm10-blacklist.bed"

@JoseEspinosa JoseEspinosa self-assigned this Jan 26, 2022
@JoseEspinosa JoseEspinosa added this to the 2.0 milestone Jan 26, 2022
This was referenced Feb 2, 2022
@JoseEspinosa
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Closed #257

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