bio-atac-seq-atac-peak-calling

Name: bio-atac-seq-atac-peak-calling
Rating: 5 (1 reviews)
Author: bg-szy

Call accessible chromatin regions from ATAC-seq BAM files using MACS3, MACS2, Genrich, or HMMRATAC. Use when identifying open chromatin from aligned ATAC-seq, choosing between point-source vs HMM peak callers, applying ENCODE-style pseudoreplicate IDR, removing blacklist regions, or fixing 501bp consensus peaks for downstream differential analysis.

1stars

Updated 18 days ago

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Version Compatibility

Reference examples tested with: MACS3 3.0.2+, MACS2 2.2.9+, Genrich 0.6.1+, HMMRATAC 1.2+ (now bundled in MACS3 as macs3 hmmratac), samtools 1.19+, bedtools 2.31+, IDR 2.0.4+.

Before using code patterns, verify installed versions match. If versions differ:

CLI: <tool> --version then <tool> --help to confirm flags

If code throws unexpected errors, introspect the installed binary (<tool> -h) and adapt the example to match the actual CLI rather than retrying.

[Description truncada. Veja o README completo no GitHub.]

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