Blacklist regions on DBA object (diffbind)
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gamma.jian • 0
@franceschinigianmarco-16472
Last seen 10 days ago
Switzerland

Hi, I am struggling to understand how to add a blacklist to my dba object. I am running the standard workflow and obtaining the message below. Despite my attempt to set blacklist to either a custom GRange (blacklist), or a constant (like DBA_BLACKLIST_GRCH37), I still get the same message: No blacklist found for the genome. Can I install a blacklist for this genome? Or how do I force the application of my GRange? Thank you


ko_dba <- dba(sampleSheet = db_df)
ko_dba <- dba.count(ko_dba, bParallel = TRUE)
ko_dba <- dba.normalize(ko_dba)
ko_dba <- dba.blacklist(ko_dba, blacklist = blacklist)

##>
Genome detected: Hsapiens.1000genomes.hs37d5
Applying blacklist...
No blacklist found for BSgenome.Hsapiens.1000genomes.hs37d5
No control reads specified, unable to generate greylist.
No intervals removed.
DiffBind chipseq • 113 views
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