ATACofthesnake 0.11.0

ATACofthesnake

ATACofthesnake

Downstream processing of ATAC data, including QC, differential accessibility -, LRT - and timecourse analyses. Optional downstream motif analyses included. Starting point are deduplicated BAM and/or CRAM files.

Important

All samples in a 'run' have to belong to the same group. That means that out of all peaks/sample, a union will be made. In case this is not relevant, you can run the workflow multiple times. Fasta headers un field 0 (space delimited) are not allowed to contain a pipe character '|' (as peaks will be delimited as such).

Installation

From pypi:

pip install ATACofthesnake

or with uv:

uv pip install ATACofthesnake

From github:

git clone [e-mail]:maxplanck-ie/ATACofthesnake.git
pixi run ATAC -h

Quickstart

ATAC -h

Bare minimum needed input:

• directory with deduplicated bam and/or cram files.
• genome fasta file
• genome annotation file (GTF format)
• read attracting regions (BED format), this is necessary and needs to contain at least the full mitochondrial chromosome.

For more details and how-to on requesting specific differential analysis and comparisons, please refer to the documentation.