damidseq_pipeline

Damiseq_pipeline is a software pipeline for automatically normalizing and reducing background noise in multiple DamID-seq FASTQ datasets. It works by adjusting read-counts for each dataset, filtering out non-aligned reads, and removing artificial biases. This helps to identify the regions of the genome bound by DNA-binding proteins accurately with next-generation sequencing data. This pipeline is open-source and available freely from the website provided.

Topic

Workflows;ChIP-seq;Microarray experiment

Detail

  • Operation: Peak calling;Standardisation and normalisation;Read binning

  • Software interface: Workflow;Script

  • Language: Perl

  • License: GNU General Public License v2

  • Cost: Free

  • Version name: 1.5.3

  • Credit: BBSRC Project Grant, a Wellcome Trust Programme.

  • Input: FASTQ

  • Output: -

  • Contact: Owen J Marshall o.marshall@gurdon.cam.ac.uk

  • Collection: -

  • Maturity: Stable

Publications

  • damidseq_pipeline: an automated pipeline for processing DamID sequencing datasets.
  • Marshall OJ and Brand AH. damidseq_pipeline: an automated pipeline for processing DamID sequencing datasets. damidseq_pipeline: an automated pipeline for processing DamID sequencing datasets. 2015; 31:3371-3. doi: 10.1093/bioinformatics/btv386
  • https://doi.org/10.1093/bioinformatics/btv386
  • PMID: 26112292
  • PMC: PMC4595905

Download and documentation

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