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.
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 the case, you can run the workflow multiple times. Fasta headers are not allowed to contain a pipe character '|' (as peaks will be delimited as such later on).
From pypi:
pip install ATACofthesnake
or with uv:
uv pip install ATACofthesnake
From github:
git clone git@github.com:maxplanck-ie/ATACofthesnake.git
pixi run ATAC -h
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.