deeptools

NGS analysis toolkit. Used for BAM to bigWig conversion, quality control (correlation, PCA, fingerprint plots), heatmaps/feature plots (TSS, peaks), suitable for ChIP-seq, RNA-seq, ATAC-seq visualization.

Quality

66%

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tessl review fix ./scientific-skills/Data Analysis/deeptools/SKILL.md

Quality

Content

57%Weight 40%Scale 1-5

Reviews the quality of instructions and guidance provided to agents. Good implementation is clear, handles edge cases, and produces reliable results.

The body is highly actionable with concrete, copy-paste-ready deepTools commands across the major assay workflows. It is held back by verbosity (templated boilerplate and inlined reference material) and missing mid-workflow validation feedback loops for batch operations.

Suggestions

Move the inlined normalization methods, effective genome sizes table, tool-command reference, and troubleshooting into the existing references/ files, keeping SKILL.md as a lean overview that links out.

Trim the templated "When to Use"/"Key Features"/"Implementation Details" boilerplate that restates the description and adds no actionable signal.

Add explicit validation checkpoints inside each analysis workflow (e.g., validate matrix.gz exists and is non-empty before plotHeatmap) with a fix→retry loop, since these are batch operations.

Dimension	Reasoning	Score
Conciseness	Noticeably verbose: templated boilerplate ("When to Use", "Key Features", "Implementation Details") restates the scope, and large reference-equivalent material (normalization methods, effective genome sizes table, tool commands, troubleshooting) is inlined rather than deferred to references/.	2 / 5
Actionability	Fully executable, copy-paste-ready commands cover the common cases — e.g. "bamCoverage --bam input.bam --outFileName output.bw --normalizeUsing RPGC --effectiveGenomeSize 2913022398 --binSize 10 --numberOfProcessors 8" and the workflow_generator invocations with full flags.	5 / 5
Workflow Clarity	Sequences are present (QC → Normalization → Comparison/Visualization, per-assay templates) with upfront file validation, but mid-workflow validation checkpoints and validate→fix→retry feedback loops are absent for these batch BAM operations, capping the score at 3.	3 / 5
Progressive Disclosure	References are real and clearly signaled one level deep (references/workflows.md, tools_reference.md, etc., all verified present), but substantial content that belongs in those references is inlined in SKILL.md, fitting the "content that should be separate is inline" anchor.	3 / 5
	Total	13 / 20 Passed

Description

75%Weight 40%Scale 1-5

Based on the skill's description, can an agent find and select it at the right time? Clear, specific descriptions lead to better discovery.

The description is specific, concrete, and distinct, with good natural trigger terms for the NGS domain. Its main weakness is the missing explicit "Use when..." guidance, which caps completeness.

Suggestions

Add an explicit "Use when..." clause naming concrete user triggers (e.g., "Use when converting BAM to bigWig, running ChIP-seq/RNA-seq/ATAC-seq QC, or generating heatmaps around TSS/peaks").

Include common file extensions (.bam, .bw, .bed, .bedGraph) so the description matches natural user phrasing including file types.

Dimension	Reasoning	Score
Specificity	Lists multiple concrete actions — "BAM to bigWig conversion", "quality control (correlation, PCA, fingerprint plots)", "heatmaps/feature plots (TSS, peaks)" — covering the toolkit comprehensively in third-person voice.	5 / 5
Completeness	Has a clear "what" but no explicit "Use when..." trigger clause; the "suitable for..." phrase only weakly implies when, which caps completeness at 3 per the guidelines.	3 / 5
Trigger Term Quality	Strong natural terms users would say ("ChIP-seq, RNA-seq, ATAC-seq", "BAM to bigWig", "heatmap"), but file extensions (.bam/.bw/.bed) and common synonyms are missing, so not a full 5.	4 / 5
Distinctiveness Conflict Risk	A clear niche (deepTools NGS analysis) with distinct assay-type triggers and minimal overlap risk with other skills.	5 / 5
	Total	17 / 20 Passed

Validation

93%

Warnings & errors only

Checks the skill against the spec for correct structure and formatting. All validation checks must pass before discovery and implementation can be scored.

Validation — 15 / 16 Passed

Validation for skill structure

Criteria	Description	Result
frontmatter_unknown_keys	Unknown frontmatter key(s) found; consider removing or moving to metadata	Warning

	Total	15 / 16 Passed

Repository: aipoch/medical-research-skills
Path: scientific-skills/Data Analysis/deeptools/SKILL.md
Commit: f5ef65b

Reviewed: ~2 hours ago

Table of Contents

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