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bedgraph-handling

separate

Generates, normalizes, and converts bedGraph signal tracks (4-column chrom/start/end/value, 0-based half-open) with bedtools genomecov, deepTools bamCoverage/bamCompare/bigwigCompare, bedtools unionbedg, and UCSC bedGraphToBigWig. Covers why a raw coverage bedGraph is not comparable across samples until normalized, the CPM/RPKM/BPM/RPGC normalization menu and the conserved-total assumption that makes them wrong under a global perturbation, the strict sorted-non-overlapping-chrom.sizes bedGraphToBigWig contract that silently corrupts a bigWig, effective-genome-size selection, and bin-size aliasing. Use when building or normalizing a coverage/signal track from a BAM, comparing tracks across samples or conditions, converting bedGraph to a browser-ready bigWig, or diagnosing a track that looks plausible but reports wrong heights.

When to use

• generating coverage/signal tracks from BAM
• normalizing tracks for cross-sample comparison
• converting bedGraph to bigWig
• diagnosing tracks with wrong heights
• selecting effective genome size
• applying CPM/RPKM/BPM/RPGC normalization

When not to use

• single-sample inspection without normalization
• distributing bedGraph as a final product
• recovering global scale without spike-in

Skill page

Source