track-generation
This skill generates normalized BigWig (.bw) tracks (and/or fold-change tracks) from BAM files for ATAC-seq and ChIP-seq visualization. It handles normalization (RPM or fold-change) and Tn5 offset correction automatically. What's more, this skill can help user visualize the signal profiles around TSS or target regions. Use this skill when you have filtered and generated the clean BAM file (e.g. `*.filtered.bam`).
npx skills add majiayu000/claude-skill-registry --skill 6-track-generation-bisnake2001-chromskills-2 --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Overview This skill converts filtered BAM files into normalized signal tracks (BigWig) for genome browser visualization. It supports both ATAC-seq and ChIP-seq datasets, automatically detecting genome assembly and chromosome size files. Main steps include: - Refer to the **Inputs & Outputs** section to check inputs and build the output architecture. All the output file should located in `${proj_dir}` in Step 0. - Always use filtered BAM file (`*.filtered.bam`) if available. - **Normalize all tracks** to 1 million mapped reads (RPM normalization). - Generate the chrom.size file. - **For ATAC-seq**, apply Tn5 offset correction (+4/−5) and generate normalized BigWig (RPM). - **For ChIP-seq**, generat RPM-normalized track without applying Tn5 offset correction - Always prompt user for whether need to visualize the signal profiles around TSS or target regions. - Visualize the signal profiles around TSS or target regions if users require. --- ## Decision Tree ### Step 0: Initialize Project Call: - `mcp__project-init-tools__project_init` with: - `sample`: all - `task`: track_generation The tool will: - Create `${sample}_track_generation` directory. - Return the full path of the `${samp
- Overview
- Decision Tree
- Step 0: Initialize Project
- Step 1: Generate Chromosome size file
- Step 2: Calculate Scaling Factor
- Step 3: Create RPM-normalized BigWig scaled to 1M mapped reads.
- Step 3: Visualize the signal profiles around TSS or target region (Optional)
What does the track-generation skill do?
This skill generates normalized BigWig (.bw) tracks (and/or fold-change tracks) from BAM files for ATAC-seq and ChIP-seq visualization. It handles normalization (RPM or fold-change) and Tn5 offset correction automatically. What's more, this skill can help user visualize the signal profiles around TSS or target regions. Use this skill when you have filtered and generated the clean BAM file (e.g. `*.filtered.bam`).
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill 6-track-generation-bisnake2001-chromskills-2 --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From majiayu000/claude-skill-registry, a repository with 534 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.