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macs3-project / MACS

MACS -- Model-based Analysis of ChIP-Seq
https://macs3-project.github.io/MACS/
BSD 3-Clause "New" or "Revised" License
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Q: single end ATAC peak calling #416

Open shokohirosue opened 4 years ago

shokohirosue commented 4 years ago

Hi, I do know that this is far from ideal, but what's your opinion about the recommended parameters for single-end ATAC seq?

Thank you so much for your help!

taoliu commented 4 years ago

@shokohirosue I personally haven't processed any single-end ATAC-seq data. But you can check the ENCODE atac-seq pipeline https://github.com/ENCODE-DCC/atac-seq-pipeline which supports both single- and paired-end data processing. I believe their strategy is to shift the read 75 basepair to the 5' end then extend it into a 150bps long fragment --shift -75 --extsize 150 --nomodel.

shokohirosue commented 4 years ago

Thank you!