StarSolo ATACseq genome Index

[akhst7]

Hi,

Kallisto bus tools uses "the DNase I Hypersensitive Sites interval list" to generate Kb ref index for ATACseq. Could anybody share tricks to generate StarSolo genome index for ATACseq ?

Thanks.

[alexdobin]

Hi @akhst7

with STAR, you can map ATAC-seq to the whole genome, no need to generate a special index.

[akhst7]

Thanks.

What I really wanted to ask was the way to generate a fragment count matrix from genome mapped bam in addition to SnapATAC (#558), which now is SnapATAC2 in python.

Hopefully, the future StarSolo can generate a fragment the count matrix or perhaps a fragment file in the bed format.

[alexdobin]

That's something I am thinking about for the future development.