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haowenz / chromap

Fast alignment and preprocessing of chromatin profiles
https://haowenz.github.io/chromap/
MIT License
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ATAC-seq single end? #152

Open lindsayhrlee opened 6 months ago

lindsayhrlee commented 6 months ago

Hi,

I understand that the default mapping option for the ATAC-seq data is pair ended, but is there a mapping option for a single ended ATAC-seq data?

Thank you, Lindsay

mourisl commented 6 months ago

Yes, you can just provide the "-1" option for single-end data.

lindsayhrlee commented 6 months ago

Thank you for your response!

Is SAM file as an output also available for ATAC-seq settings? or is this only limited to Hi-C?

mourisl commented 6 months ago

Yes, the SAM format is supported for all the sequencing platforms.