Wrong parameters for MACS2

[suragnair]

https://github.com/r3fang/SnapATAC/blob/c3ab177558f0fe9c47cbd68969df7b06de5b07d9/R/runMACS.R#L32

According to the MACS2 page the settings --shift -100 --extsize 200 should be used for DNase-seq/ATAC-seq data.

--nomodel --shift 37 --extsize 73 should be used for nuclesome-seq data.

[hjack123]

The webpage doesn't say ATAC-seq data though. I don't think DNase-seq is equivalent to ATAC-seq?

[nes-b]

Have a look at this issue: https://github.com/taoliu/MACS/issues/331

Followig this argumentation, it should be reasonable to use DNase-seq equivalent params. Instead, scaling to --shift -75 --extsize 150 might be biologically appropriate, too.

[suragnair]

The above is correct. ENCODE also uses --shift -75 --extsize 150.