nucleosome-positioning

Name: nucleosome-positioning
Author: GPTomics

1.1kstars185forks

How to install nucleosome-positioning?

gptomics/bioskills/nucleosome-positioning

$npx -y skills add GPTomics/bioSkills --skill nucleosome-positioning

Installs into the current project.

Summary

Map nucleosome center positions, occupancy, and fuzziness from ATAC-seq fragment-size patterns using NucleoATAC, ATACseqQC, DANPOS3, or scprinter. Use when characterizing nucleosome organization at promoters and enhancers, calling +1/-1 nucleosomes flanking NFRs, generating V-plo

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SKILL.md

1	## Version Compatibility
2
3	Reference examples tested with: NucleoATAC 0.3.4+, ATACseqQC 1.26+, DANPOS 3.1+, samtools 1.19+, pysam 0.22+, pyBigWig 0.3+, BSgenome.Hsapiens.UCSC.hg38 1.4+, TxDb.Hsapiens.UCSC.hg38.knownGene 3.18+.
4
5	NucleoATAC is unmaintained since 2018 but remains the canonical ATAC-specific nucleosome caller; ATACseqQC, DANPOS3, and scprinter are actively developed alternatives. Verify versions before use:
6	- Python: `pip show <package>` then `help(module.function)` to check signatures
7	- R: `packageVersion('<pkg>')` then `?function_name` to verify parameters
8	- CLI: `<tool> --version` then `<tool> --help` to confirm flags
9
10	If code throws unexpected errors, introspect the installed package and adapt rather than retrying.
11
12	# Nucleosome Positioning
13
14	"Where are the nucleosomes in my ATAC-seq data?" -> Use fragment-size classes (Tn5 cuts twice through naked DNA generating short fragments; once on each side of a single nucleosome generating ~147+linker fragments) to call nucleosome centers, occupancy scores, and the spacing pattern around regulatory elements.
15
16	- CLI: `nucleoatac run --bed regions.bed --bam sample.bam --fasta genome.fa`
17	- R: `ATACseqQC::splitGAlignmentsByCut()` -> fragment classes; `factorFootprints()` -> per-TF flanking nuc analysis
18	- CLI: `python danpos.py dpos sample.bam` (alternative; supports MNase, ATAC, DNase)
19	- Python: `scprinter` for multi-scale nucleosome inference
20
21	## Nucleosome Physics for ATAC
22
23	A nucleosome wraps ~147 bp DNA in 1.65 turns. Adjacent nucleosomes are separated by 20-50 bp linker; mean nucleosome repeat length (NRL) is species-dependent:
24
25	\| Cell type / organism \| NRL \| Notes \|
26	\|----------------------\|-----\|-------\|
27	\| Yeast S. cerevisiae \| 165 bp \| Tightly packed; less linker \|
28	\| Drosophila S2 \| 175-185 bp \| \|
29	\| Mouse ES cells \| 188-196 bp \| \|
30	\| Human HEK293 / K562 \| 196-200 bp \| Standard somatic \|
31	\| Human cortical neurons \| 211 bp \| Longer linker \|
32	\| Sperm chromatin \| 240-250 bp \| Tight packaging via protamines \|
33	\| Active gene bodies \| -10 bp shorter than genome avg \| Active transcription disrupts \|
34
35	NRL determines fragment-size peak positions. ATAC mono-nucleosome peak is at NRL (NOT 147 bp -- that's the protected length; ATAC fragments span the full nucleosome+linker). Di-nuc is at 2x NRL minus a small overlap.
36
37	## Fragment-Size Classes (Buenrostro 2013, refined)
38
39	\| Class \| Fragment range \| Origin \| Use \|
40	\|-------\|---------------\|--------\|-----\|
41	\| Sub-nucleosomal / NFR \| < 100 bp \| Two Tn5 cuts in naked accessible DNA \| TF binding, footprinting \|
42	\| Mono-nucleosomal \| 180-247 bp \| Tn5 cuts on each side of one nucleosome \| Nucleosome positioning \|
43	\| Di-nucleosomal \| 315-473 bp \| Tn5 cuts span two nucleosomes \| Phasing, NRL estimation \|
44	\| Tri-nucleosomal \| 558-615 bp \| Three nucleosomes \| Heterochromatin / phasing \|
45	\| > 700 bp \| Rare \| Often artefact (chimeric); discard \| -- \|
46
47	Mono-nucleosome window 180-247 bp is the Buenrostro 2013 convention; ATACseqQC uses 180-250. Adjust for the target organism's NRL.
48
49	## V-Plot Interpretation
50
51	V-plots (fragment-size vs position) are diagnostic. X-axis is position relative to a feature (TSS, motif center); Y-axis is fragment size. Aggregate density forms characteristic patterns:
52
53	\| Pattern \| Visual \| Meaning \|
54	\|---------\|--------\|---------\|
55	\| V (apex at center, low size at center, increasing flanks) \| Classic V \| TF or NFR at center, flanking nucleosomes \|
56	\| W (two V's flanking center) \| W-shape \| NFR at center plus +1 / -1 nucleosomes \|
57	\| Inverted V (peak at center) \| Mountain \| Fragment fully enclosed at feature; e.g. nucleosome-bound TF \|
58	\| Flat band at 200 bp \| Horizontal line \| Constitutive nucleosome (no positioning relative to feature) \|
59	\| 10.4 bp helical phasing on V \| Sub-peaks at 50, 60, 70, 80 bp size \| Tn5 helical preference visible; high-quality library \|
60
61	V-plots are the primary diagnostic for whether nucleosome-positioning analysis will succeed. Flat-band patterns mean no positioning information; classic V/W patterns mean positioning is recoverable.
62
63	## Algorithmic Taxonomy
64
65	\| Tool \| Method \| Resolution \| Strength \| Fails when \|
66	\|------\|--------\|-----------\|----------\|------------\|
67	\| NucleoATAC \| Cross-correlation with idealized V-plot template; per-base occupancy + nucleosome calls \| Single-bp \| ATAC-specific; provides occupancy + fuzziness \| Unmaintained since 2018; pegs Python 2/3.6; struggles on chromatin without clear NRL \|
68	\| ATACseqQC \| Fragment-size split + Tn5-shifted GAlignments + V-plot from BAM \| Region-level \| R/B

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nucleosome-positioning

1.1kstars185forks

View on GitHub

How to install nucleosome-positioning?

gptomics/bioskills/nucleosome-positioning

$npx -y skills add GPTomics/bioSkills --skill nucleosome-positioning

Installs into the current project.

Summary

Files · 1

View on GitHub

SKILL.md

1	## Version Compatibility
2
3	Reference examples tested with: NucleoATAC 0.3.4+, ATACseqQC 1.26+, DANPOS 3.1+, samtools 1.19+, pysam 0.22+, pyBigWig 0.3+, BSgenome.Hsapiens.UCSC.hg38 1.4+, TxDb.Hsapiens.UCSC.hg38.knownGene 3.18+.
4
5	NucleoATAC is unmaintained since 2018 but remains the canonical ATAC-specific nucleosome caller; ATACseqQC, DANPOS3, and scprinter are actively developed alternatives. Verify versions before use:
6	- Python: `pip show <package>` then `help(module.function)` to check signatures
7	- R: `packageVersion('<pkg>')` then `?function_name` to verify parameters
8	- CLI: `<tool> --version` then `<tool> --help` to confirm flags
9
10	If code throws unexpected errors, introspect the installed package and adapt rather than retrying.
11
12	# Nucleosome Positioning
13
14	"Where are the nucleosomes in my ATAC-seq data?" -> Use fragment-size classes (Tn5 cuts twice through naked DNA generating short fragments; once on each side of a single nucleosome generating ~147+linker fragments) to call nucleosome centers, occupancy scores, and the spacing pattern around regulatory elements.
15
16	- CLI: `nucleoatac run --bed regions.bed --bam sample.bam --fasta genome.fa`
17	- R: `ATACseqQC::splitGAlignmentsByCut()` -> fragment classes; `factorFootprints()` -> per-TF flanking nuc analysis
18	- CLI: `python danpos.py dpos sample.bam` (alternative; supports MNase, ATAC, DNase)
19	- Python: `scprinter` for multi-scale nucleosome inference
20
21	## Nucleosome Physics for ATAC
22
23	A nucleosome wraps ~147 bp DNA in 1.65 turns. Adjacent nucleosomes are separated by 20-50 bp linker; mean nucleosome repeat length (NRL) is species-dependent:
24
25	\| Cell type / organism \| NRL \| Notes \|
26	\|----------------------\|-----\|-------\|
27	\| Yeast S. cerevisiae \| 165 bp \| Tightly packed; less linker \|
28	\| Drosophila S2 \| 175-185 bp \| \|
29	\| Mouse ES cells \| 188-196 bp \| \|
30	\| Human HEK293 / K562 \| 196-200 bp \| Standard somatic \|
31	\| Human cortical neurons \| 211 bp \| Longer linker \|
32	\| Sperm chromatin \| 240-250 bp \| Tight packaging via protamines \|
33	\| Active gene bodies \| -10 bp shorter than genome avg \| Active transcription disrupts \|
34
35	NRL determines fragment-size peak positions. ATAC mono-nucleosome peak is at NRL (NOT 147 bp -- that's the protected length; ATAC fragments span the full nucleosome+linker). Di-nuc is at 2x NRL minus a small overlap.
36
37	## Fragment-Size Classes (Buenrostro 2013, refined)
38
39	\| Class \| Fragment range \| Origin \| Use \|
40	\|-------\|---------------\|--------\|-----\|
41	\| Sub-nucleosomal / NFR \| < 100 bp \| Two Tn5 cuts in naked accessible DNA \| TF binding, footprinting \|
42	\| Mono-nucleosomal \| 180-247 bp \| Tn5 cuts on each side of one nucleosome \| Nucleosome positioning \|
43	\| Di-nucleosomal \| 315-473 bp \| Tn5 cuts span two nucleosomes \| Phasing, NRL estimation \|
44	\| Tri-nucleosomal \| 558-615 bp \| Three nucleosomes \| Heterochromatin / phasing \|
45	\| > 700 bp \| Rare \| Often artefact (chimeric); discard \| -- \|
46
47	Mono-nucleosome window 180-247 bp is the Buenrostro 2013 convention; ATACseqQC uses 180-250. Adjust for the target organism's NRL.
48
49	## V-Plot Interpretation
50
51	V-plots (fragment-size vs position) are diagnostic. X-axis is position relative to a feature (TSS, motif center); Y-axis is fragment size. Aggregate density forms characteristic patterns:
52
53	\| Pattern \| Visual \| Meaning \|
54	\|---------\|--------\|---------\|
55	\| V (apex at center, low size at center, increasing flanks) \| Classic V \| TF or NFR at center, flanking nucleosomes \|
56	\| W (two V's flanking center) \| W-shape \| NFR at center plus +1 / -1 nucleosomes \|
57	\| Inverted V (peak at center) \| Mountain \| Fragment fully enclosed at feature; e.g. nucleosome-bound TF \|
58	\| Flat band at 200 bp \| Horizontal line \| Constitutive nucleosome (no positioning relative to feature) \|
59	\| 10.4 bp helical phasing on V \| Sub-peaks at 50, 60, 70, 80 bp size \| Tn5 helical preference visible; high-quality library \|
60
61	V-plots are the primary diagnostic for whether nucleosome-positioning analysis will succeed. Flat-band patterns mean no positioning information; classic V/W patterns mean positioning is recoverable.
62
63	## Algorithmic Taxonomy
64
65	\| Tool \| Method \| Resolution \| Strength \| Fails when \|
66	\|------\|--------\|-----------\|----------\|------------\|
67	\| NucleoATAC \| Cross-correlation with idealized V-plot template; per-base occupancy + nucleosome calls \| Single-bp \| ATAC-specific; provides occupancy + fuzziness \| Unmaintained since 2018; pegs Python 2/3.6; struggles on chromatin without clear NRL \|
68	\| ATACseqQC \| Fragment-size split + Tn5-shifted GAlignments + V-plot from BAM \| Region-level \| R/B

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