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atac-peak-calling

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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.

When to use

• identifying open chromatin from aligned ATAC-seq
• choosing between point-source vs HMM peak callers
• applying ENCODE-style pseudoreplicate IDR
• removing blacklist regions
• fixing 501bp consensus peaks for downstream differential analysis

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