Chunk #63 — Methods — Statistical filtering and analysis — Replicate bias

Source

Shining a light on dark sequencing: characterising errors in Ion Torrent PGM data.

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To prevent reference end-effects and repeat-effects, we used repeat-masked data and ignored the first and last 120 bp of the reference genome. We visually identified whether the distribution of read starting position (5′ aligned position) on the reference genome was uniformly distributed for each individual run.