ChIP-Seq Mapper

Maps ChIP and input reads onto RepeatExplorer2 clusters and compares their abundance in each. Repeats bound by the protein under study are enriched in the ChIP sample relative to the input, which identifies them without needing an assembled reference. It has been used to find centromeric repeats through CENH3 ChIP-seq.

Output

• Per-cluster ratio of ChIP to input read counts
• A ranking of clusters by enrichment, identifying the associated repeats