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I read the README and it was briefly mentioned that one can use the switch dnase instead of atac to use this pipeline with single-end DNAse-seq data. A test run I did yesterday with my own data completed successfully, but a quick look at the croo-generated html seems to suggest that dnase sequencing reads are processed pretty much similarly to atac-seq. I do not have much experience in DNAse-seq so far, so I need some clarification when using this pipeline with DNAse-seq sequencing data.
Is Dnase-I bias cleavage bias correction done when setting the option dnase in the pipeline input JSON?
My assumption is the macs2 was run with the parameters optimized for Dnase-seq data? So the output peak files can directly be used for downstream analysis to infer 'Dnase hypersensitive regions' == accessible chromatin regions?
The text was updated successfully, but these errors were encountered:
I read the
README
and it was briefly mentioned that one can use the switchdnase
instead ofatac
to use this pipeline with single-end DNAse-seq data. A test run I did yesterday with my own data completed successfully, but a quick look at thecroo
-generatedhtml
seems to suggest that dnase sequencing reads are processed pretty much similarly to atac-seq. I do not have much experience in DNAse-seq so far, so I need some clarification when using this pipeline with DNAse-seq sequencing data.dnase
in the pipeline input JSON?The text was updated successfully, but these errors were encountered: