PeakSeq: a program for identifying and ranking peak regions in ChIP-Seq

PeakSeq is a program developed by Mark Gerstein’ lab for identifying and ranking peak regions in ChIP-Seq experiments. It takes as input, mapped reads from a ChIP-Seq experiment, mapped reads from a control experiment and outputs a file with peak regions ranked with increasing Q-values.

PeakSeq uses  two-pass strategy compensates for signal caused by open chromatin, as revealed by inclusion of the controls. The first pass identifies putative binding sites and compensates for genomic variation in the ‘mappability’ of sequences. The second pass filters out sites not significantly enriched compared to the normalized control, computing precise enrichments and significances. The scoring procedure is  to optimize experimental design by estimating the depth of sequencing required for a desired level of coverage and demonstrating that more than two replicates provides only a marginal gain in information.

PeakSeq dumps a narrowPeak file  and a txt file with peaks. The peak region, p-value, q-value, and enrichment statistics are reported in the output file.

Incoming search terms:

  • illumina miseq peak
  • narrowpeak file
  • peakseq narrowpeak
  • R package PeakSeq

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