damidseq_pipeline: An Automated Pipeline for Processing DamID Sequencing Datasets

Bioinformatics. 2015 Oct 15;31(20):3371-3. doi: 10.1093/bioinformatics/btv386. Epub 2015 Jun 25.

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.

Availability and implementation: 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).

Contact: o.marshall@gurdon.cam.ac.uk

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • DNA-Binding Proteins / metabolism*
  • High-Throughput Nucleotide Sequencing / methods
  • Sequence Analysis, DNA / methods*
  • Software*

Substances

  • DNA-Binding Proteins