Build chromatin accessibility maps
accessibility-aggregationskillsetup L2★35
ammawla/encode-toolkit ↗What it does
Aggregate chromatin accessibility peaks across experiments
Best for
Building comprehensive open chromatin maps from multiple ATAC-seq and DNase-seq experiments.
Inputs
- · narrowPeak BED files list
- · ENCODE experiment accessions
- · Tissue/cell-type filter
Outputs
- · Union peak set BED
- · Quality metrics CSV
- · Aggregation report
Requires
- · bedtools
- · ENCODE REST API
- · ENCODE Blacklist v2
Preconditions
- · GRCh38/hg38 assembly consistent
- · Valid narrowPeak format
Failure modes
- · Mixed assemblies
- · Missing peaks
- · Blacklist region overlap
Trust signals
- · Corces et al. 2017 (733 citations)
- · ENCODE Blacklist Amemiya 2019