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10XGenomics / cellranger

10x Genomics Single Cell Analysis
https://www.10xgenomics.com/support/software/cell-ranger
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dnase peaks information #136

Closed rtyags closed 11 months ago

rtyags commented 3 years ago

Hi,

I notice that v2.0 doesn't include dnase.bed information, leading to all 0s in the result table. Is there a reason why this was removed? Can I use a custom reference with dnase.bed file included?

Thanks

brettolsen commented 2 years ago

We found that the DNAse reference files were not a very good control / match for scATAC and so removed them from our provided references. If you provide a custom reference with your own dnase.bed then it should run without any trouble.