Route: chip-pairs-peaks

Peak calling for the chip results.

Usage

After individual samples are processed with the chip route, manually define the peak type in settings.txt and treatment-control pairs in the samples.pairs.csv sample sheet.

ChIP-seq can be used to detect transcription factor binding sites (narrow peaks) as well as enriched regions associated with most histone modification (broad peaks). According to the ENCODE standards, broad marks include H3F3A, H3K27me3, H3K36me3, H3K4me1, H3K79me2, H3K79me3, H3K9me1, H3K9me2, and H4K20me1. Narrow marks include H2AFZ, H3ac, H3K27ac, H3K4me2, H3K4me3, and H3K9ac.

The sample sheet requires a treatment and a control (genomic input or mock IP) sample. If no control is available, specify the same sample in both columns.

Run chip-pairs-peaks route from the same directory as chip.

sns/run chip-pairs-peaks

Output

Primary results:

• peaks-*: Peaks.