Validate and process sequencing coverage files for normalization, QC, and visualization.
npx skills add https://github.com/dralkh/seerai --skill deeptools-dralkh
Please help me install this Agent Skill. Skill: deeptools Source: https://github.com/dralkh/seerai/tree/main/skills/deeptools Command: npx skills add https://github.com/dralkh/seerai --skill deeptools-dralkh
deepTools removes the manual complexity of turning BAM files into interpretable sequencing quality control and visualization outputs, making it easier to compare samples and inspect signal across genomic features.
Use the deeptools skill to validate your BAM, bigWig, and BED files, then generate the appropriate ChIP-seq, RNA-seq, or ATAC-seq workflow for your dataset.
High-intent search queries and answers about installing and using this skill.
BAM to bigWig conversion uses bamCoverage to generate normalized coverage tracks. You apply RPGC normalization with effective genome sizes and read filtering to create accurate bigWig files for ChIP-seq and ATAC-seq visualization.
You can generate TSS heatmaps and profile plots from bigWig files by building coverage matrices around transcription start sites. This region-based visualization produces publication-ready figures showing signal enrichment across genomic features.
Assessing ChIP-seq replicate quality involves correlation plots, PCA, and fingerprint analysis to measure replicate similarity and library complexity. These QC steps inspect ChIP enrichment and fragment size across BAM file inputs.
Indexed BAM files are required inputs for RNA-seq QC and log2 sample comparison. The workflow validates BAM, bigWig, and BED inputs before generating reusable analysis templates for reproducible command-line processing.
NGS coverage normalization fails without effective genome sizes because RPGC normalization requires this parameter to calculate reads per genomic content. You must provide the correct effective genome size for your specific reference assembly during bigWig generation.
deepTools supports RNA-seq, ChIP-seq, and ATAC-seq workflows within a single pipeline. It applies appropriate normalization methods for each NGS assay type, enabling coverage generation, QC, and visualization across multiple sequencing workflows.
hxk622Convert BAM files to bigWig and generate genomic heatmaps.
shushuznConvert BAM alignments into normalized bigWig coverage tracks and generate QC plots.
SologaConvert BAM files to normalized bigWig tracks and generate quality control metrics.
ovachieverConvert BAM alignments into normalized coverage tracks and generate QC metrics.
