atac-peak-calling

Name: atac-peak-calling
Author: GPTomics

1.1kstars185forks

How to install atac-peak-calling?

gptomics/bioskills/atac-peak-calling

$npx -y skills add GPTomics/bioSkills --skill atac-peak-calling

Installs into the current project.

Summary

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,

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SKILL.md

1	## Version Compatibility
2
3	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+.
4
5	Before using code patterns, verify installed versions match. If versions differ:
6	- CLI: `<tool> --version` then `<tool> --help` to confirm flags
7
8	If code throws unexpected errors, introspect the installed binary (`<tool> -h`) and adapt the example to match the actual CLI rather than retrying.
9
10	# ATAC-seq Peak Calling
11
12	"Call accessible regions from my ATAC-seq BAM" -> Identify Tn5-hypersensitive open chromatin, treating fragments as point insertion events (not protein-bound regions as in ChIP-seq) and accounting for the lack of input control.
13
14	- CLI (canonical, ENCODE 4): `macs2 callpeak -t atac.bam -f BAM -g hs -n sample --nomodel --shift -75 --extsize 150 --keep-dup all -B --SPMR -p 0.01` (use `-f BAM`, not `-f BAMPE` -- BAMPE reads true fragment ends and ignores `--shift`/`--extsize`)
15	- CLI (HMM-based, single sample): `macs3 hmmratac -i atac.bam -n sample --outdir hmm_out`
16	- CLI (joint replicates): `Genrich -j -t rep1.bam,rep2.bam -o peaks.narrowPeak -e chrM -E blacklist.bed`
17
18	The `-p 0.01` (loose) plus IDR is the ENCODE pattern: low stringency increases peak overlap between replicates, and IDR rescues the reproducible set. Single-sample workflows usually swap to `-q 0.05` instead.
19
20	## Algorithmic Taxonomy
21
22	\| Tool \| Model \| Treats fragments as \| Min reps \| Strength \| Fails when \|
23	\|------\|-------\|---------------------\|----------\|----------\|------------\|
24	\| MACS3/MACS2 \| Local Poisson lambda + FDR \| Point-source insertions (+/- shift) \| 1 \| Mature, ENCODE-default, fast, narrow + broad modes \| Confounds NFR with broad accessible domains; no input means lambda from local genome only \|
25	\| Genrich (ATAC mode -j) \| q-value on log-transformed p-value, joint replicate model \| Whole fragments (paired-end intervals) \| 1 (multi-rep optional) \| Treats reps jointly; can exclude chrM via `-e chrM`; auto blacklist via `-E`; PCR-dup removal via `-r` \| Less peer-reviewed than MACS; thin literature; slow on deep libraries \|
26	\| MACS3 hmmratac (was HMMRATAC) \| 3-state HMM (open / nucleosomal / background) on fragment-size signal \| Fragment-size classes \| 1 \| Models nucleosome periodicity directly; differentiates NFR and flanking nucleosomes \| Needs >= 30M de-duplicated nuclear reads; memory-hungry; slow; flat fragment distribution -> garbage HMM \|
27	\| HOMER `findPeaks -style dnase` \| Fixed window + fold-change cutoff \| Tag positions \| 1 \| Convenient for downstream HOMER motif analysis \| Less calibrated p-values than MACS; window-size sensitive \|
28	\| nf-core/atacseq \| Wrapper (MACS2 by default) \| Same as MACS2 \| 1 \| Reproducible Nextflow pipeline with QC built in \| Only as good as the underlying caller \|
29
30	Methodology evolves; verify the current ENCODE ATAC-seq Standards (encodeproject.org pipelines/atac-seq) before locking parameters. ENCODE 4 still defaults to MACS2 (not MACS3) at time of writing; `macs3 callpeak` is API-compatible for ATAC parameters but not yet the official ENCODE binary.
31
32	## Shift-Extend vs BAMPE: The Critical Choice
33
34	Two valid ways to feed paired-end ATAC into MACS:
35
36	Pattern A (ENCODE / "single-end-ified"): `-f BAMPE` actually IGNORES `--shift/--extsize`. To activate them, use `-f BAM` and treat each end independently. ENCODE's pipeline uses `-f BAM --shift -75 --extsize 150` to model each Tn5 cut as a 150 bp window centered on the insertion site, ignoring fragment lengths.
37
38	Pattern B (paired-fragment): `-f BAMPE` uses the full paired-end fragment span as the signal interval. Best when fragment lengths are biologically meaningful (e.g., NFR-only peak calling at 38/75 bp). In BAMPE mode, do NOT set `--shift/--extsize` (silently ignored, but confusing).
39
40	For most bulk ATAC, Pattern A matches ENCODE convention and is reproducible against published peak sets. Pattern B can be more sensitive at narrow regulatory elements but does not match ENCODE outputs.
41
42	## Effective Genome Size
43
44	`-g hs` and `-g mm` are MACS shorthands for old defaults. Modern values:
45
46	\| Genome \| MACS shorthand \| Actual mappable size \| Source \|
47	\|--------\|---------------\|----------------------\|--------\|
48	\| hg38 \| `-g hs` (2.7e9) \| 2.701e9 (50bp), 2.748e9 (75bp), 2.806e9 (100bp), 2.862e9 (150bp) \| deepTools `effectiveGenomeSize` \|
49	\| hg19 \| `-g hs` (2.7e9) \| 2.686e9 (50bp), 2.777e9 (100bp) \| deepTools \|
50	\| mm10 \| `-g mm` (1.87e9) \| 2.308e9 (50bp), 2.408e9 (75bp), 2.467e9 (100bp) \| deepTools \|
51	\| mm39 \| no

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atac-peak-calling

1.1kstars185forks

View on GitHub

How to install atac-peak-calling?

gptomics/bioskills/atac-peak-calling

$npx -y skills add GPTomics/bioSkills --skill atac-peak-calling

Installs into the current project.

Summary

Files · 1

View on GitHub

SKILL.md

1	## Version Compatibility
2
3	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+.
4
5	Before using code patterns, verify installed versions match. If versions differ:
6	- CLI: `<tool> --version` then `<tool> --help` to confirm flags
7
8	If code throws unexpected errors, introspect the installed binary (`<tool> -h`) and adapt the example to match the actual CLI rather than retrying.
9
10	# ATAC-seq Peak Calling
11
12	"Call accessible regions from my ATAC-seq BAM" -> Identify Tn5-hypersensitive open chromatin, treating fragments as point insertion events (not protein-bound regions as in ChIP-seq) and accounting for the lack of input control.
13
14	- CLI (canonical, ENCODE 4): `macs2 callpeak -t atac.bam -f BAM -g hs -n sample --nomodel --shift -75 --extsize 150 --keep-dup all -B --SPMR -p 0.01` (use `-f BAM`, not `-f BAMPE` -- BAMPE reads true fragment ends and ignores `--shift`/`--extsize`)
15	- CLI (HMM-based, single sample): `macs3 hmmratac -i atac.bam -n sample --outdir hmm_out`
16	- CLI (joint replicates): `Genrich -j -t rep1.bam,rep2.bam -o peaks.narrowPeak -e chrM -E blacklist.bed`
17
18	The `-p 0.01` (loose) plus IDR is the ENCODE pattern: low stringency increases peak overlap between replicates, and IDR rescues the reproducible set. Single-sample workflows usually swap to `-q 0.05` instead.
19
20	## Algorithmic Taxonomy
21
22	\| Tool \| Model \| Treats fragments as \| Min reps \| Strength \| Fails when \|
23	\|------\|-------\|---------------------\|----------\|----------\|------------\|
24	\| MACS3/MACS2 \| Local Poisson lambda + FDR \| Point-source insertions (+/- shift) \| 1 \| Mature, ENCODE-default, fast, narrow + broad modes \| Confounds NFR with broad accessible domains; no input means lambda from local genome only \|
25	\| Genrich (ATAC mode -j) \| q-value on log-transformed p-value, joint replicate model \| Whole fragments (paired-end intervals) \| 1 (multi-rep optional) \| Treats reps jointly; can exclude chrM via `-e chrM`; auto blacklist via `-E`; PCR-dup removal via `-r` \| Less peer-reviewed than MACS; thin literature; slow on deep libraries \|
26	\| MACS3 hmmratac (was HMMRATAC) \| 3-state HMM (open / nucleosomal / background) on fragment-size signal \| Fragment-size classes \| 1 \| Models nucleosome periodicity directly; differentiates NFR and flanking nucleosomes \| Needs >= 30M de-duplicated nuclear reads; memory-hungry; slow; flat fragment distribution -> garbage HMM \|
27	\| HOMER `findPeaks -style dnase` \| Fixed window + fold-change cutoff \| Tag positions \| 1 \| Convenient for downstream HOMER motif analysis \| Less calibrated p-values than MACS; window-size sensitive \|
28	\| nf-core/atacseq \| Wrapper (MACS2 by default) \| Same as MACS2 \| 1 \| Reproducible Nextflow pipeline with QC built in \| Only as good as the underlying caller \|
29
30	Methodology evolves; verify the current ENCODE ATAC-seq Standards (encodeproject.org pipelines/atac-seq) before locking parameters. ENCODE 4 still defaults to MACS2 (not MACS3) at time of writing; `macs3 callpeak` is API-compatible for ATAC parameters but not yet the official ENCODE binary.
31
32	## Shift-Extend vs BAMPE: The Critical Choice
33
34	Two valid ways to feed paired-end ATAC into MACS:
35
36	Pattern A (ENCODE / "single-end-ified"): `-f BAMPE` actually IGNORES `--shift/--extsize`. To activate them, use `-f BAM` and treat each end independently. ENCODE's pipeline uses `-f BAM --shift -75 --extsize 150` to model each Tn5 cut as a 150 bp window centered on the insertion site, ignoring fragment lengths.
37
38	Pattern B (paired-fragment): `-f BAMPE` uses the full paired-end fragment span as the signal interval. Best when fragment lengths are biologically meaningful (e.g., NFR-only peak calling at 38/75 bp). In BAMPE mode, do NOT set `--shift/--extsize` (silently ignored, but confusing).
39
40	For most bulk ATAC, Pattern A matches ENCODE convention and is reproducible against published peak sets. Pattern B can be more sensitive at narrow regulatory elements but does not match ENCODE outputs.
41
42	## Effective Genome Size
43
44	`-g hs` and `-g mm` are MACS shorthands for old defaults. Modern values:
45
46	\| Genome \| MACS shorthand \| Actual mappable size \| Source \|
47	\|--------\|---------------\|----------------------\|--------\|
48	\| hg38 \| `-g hs` (2.7e9) \| 2.701e9 (50bp), 2.748e9 (75bp), 2.806e9 (100bp), 2.862e9 (150bp) \| deepTools `effectiveGenomeSize` \|
49	\| hg19 \| `-g hs` (2.7e9) \| 2.686e9 (50bp), 2.777e9 (100bp) \| deepTools \|
50	\| mm10 \| `-g mm` (1.87e9) \| 2.308e9 (50bp), 2.408e9 (75bp), 2.467e9 (100bp) \| deepTools \|
51	\| mm39 \| no

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