How to specify more than 2 DHS replication ?

broadinstitute / ABC-Enhancer-Gene-Prediction

Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)

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How to specify more than 2 DHS replication ? #234

Closed nttg8100 closed 2 months ago

nttg8100 commented 2 months ago

On the NG2019, the supplementary showed that it has 2 bio replications for DHS. However, the script does not show me that I can specify by adding "," if I have more than one samples. It can be used for the H3K27ac but not for the accessibility bam file (DHS or ATAC). Am I misunderstanding about the pipeline ? If I'm correct, what should I do:

Use only one because the performance is similar
Remap or combine 2 replications to be one bam file

nttg8100 commented 2 months ago

I found that the current ABC does not support this but I can manually combine the candidate regions from bed files, then merge them into one.