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deepTools NGS Analysis

Guides an agent through deepTools commands for BAM-to-bigWig conversion, QC, and genomic heatmaps

Source Download skill
Repository
K-Dense-AI/scientific-agent-skills
Stars
55,780
Licence
MIT
Files
10 files

What it does

This skill gives an AI agent detailed knowledge of deepTools, a command-line toolkit that turns sequencing alignment files (BAM) into coverage tracks (bigWig), runs quality checks such as correlation, PCA and fingerprint plots, and draws heatmaps and profiles around genes or peaks. Once installed, the agent can pick the right normalization, write the commands for common ChIP-seq, RNA-seq and ATAC-seq workflows, and check input files before analysis. It also includes two helper scripts: one validates BAM, bigWig and BED files, and one generates bash workflow templates.

Great for

  • Bioinformaticians running ChIP-seq, ATAC-seq or RNA-seq visualization and QC
  • Students learning how normalization and genome-size choices affect coverage tracks
  • Labs that need a reproducible starting script for standard deepTools pipelines

Skip it if

  • Clinical or diagnostic decisions: the validation script does not confirm assembly identity or biological suitability, so outputs need expert review
  • Users without sequencing data or command-line experience, since the skill assumes alignment files and a Python environment
  • Gene-level RNA-seq quantification: the skill itself notes bamCoverage RPKM scales genomic bins, not genes

Try asking

  • “Convert my ChIP-seq BAM files to normalized bigWig tracks with CPM”
  • “Check whether my replicate ChIP BAMs correlate and make a PCA plot”
  • “Create a heatmap of signal around TSS from my bigWig and BED files”
  • “Generate a ChIP-seq QC bash workflow for my input and ChIP BAMs”
Step-by-step guide: how to use deepTools NGS AnalysisInstall, first run, examples, tips and FAQs

Install in 3 steps

  1. 1

    Download the skill

    The ZIP contains the 10 original files, the MIT licence and an attribution note.

    deeptools.zip
  2. 2

    Add it to your agent

    Claude Code (all projects)

    mkdir -p ~/.claude/skills && unzip deeptools.zip -d ~/.claude/skills/

    Claude Code / Agent SDK (this project only)

    mkdir -p .claude/skills && unzip deeptools.zip -d .claude/skills/

    Claude apps (web/desktop): Settings → Capabilities → Skills → Upload skill, and choose the ZIP.

  3. 3

    Ask for the task

    No special command needed — the agent reads the skill's description and loads it when your request matches. Try one of the prompts above.

Get better results

  • Run scripts/validate_files.py on your BAM, bigWig and BED files before any analysis to catch missing indexes and malformed rows
  • Choose the effective genome size that matches your exact FASTA and filtering policy rather than copying a table value blindly
  • Review the generated workflow script before running it, since it executes shell commands on your data

What's inside

  • assets/quick_reference.md
  • references/core_workflows.md
  • references/effective_genome_sizes.md
  • references/normalization_methods.md
  • references/review.md
  • references/tools_reference.md
  • references/workflows.md
  • scripts/validate_files.py
  • scripts/workflow_generator.py
  • SKILL.md

Redistributed unmodified from K-Dense-AI/scientific-agent-skills under the MIT licence. The assessment was drafted with AI from the skill's files on 2026-10-29. Skills can instruct your agent to run code — read SKILL.md and any scripts before installing.