title: damidseq_pipeline: an automated pipeline for processing DamID sequencing datasets.
abstract: DamID is a powerful technique for identifying regions of the genome bound by a DNA-binding (or DNA-associated) protein. Currently, no method exists for automatically processing next-generation sequencing DamID (DamID-seq) data, and the use of DamID-seq datasets with normalization based on read-counts alone can lead to high background and the loss of bound signal. DamID-seq thus presents novel challenges in terms of normalization and background minimization. We describe here damidseq_pipeline, a software pipeline that performs automatic normalization and background reduction on multiple DamID-seq FASTQ datasets.
  
  
  METHODS
  Open-source and freely available from http://owenjm.github.io/damidseq_pipeline. The damidseq_pipeline is implemented in Perl and is compatible with any Unix-based operating system (e.g. Linux, Mac OSX).
  
  
  BACKGROUND
  o.marshall@gurdon.cam.ac.uk
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Wellcome Trust/Cancer Research UK Gurdon Institute, Cambridge, CB2 1QN, UK.
authors.forename: Owen J
authors.initials: OJ
authors.lastname: Marshall
authors.affiliation: Wellcome Trust/Cancer Research UK Gurdon Institute, Cambridge, CB2 1QN, UK.
authors.forename: Andrea H
authors.initials: AH
authors.lastname: Brand
mesh_terms: D001665:Binding Sites; D004268:DNA-Binding Proteins / Q000378:metabolism*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
chemical_list: D004268:DNA-Binding Proteins