damidseq_pipeline: an automated pipeline for processing DamID sequencing datasets.


Change log
Authors
Marshall, Owen J 
Brand, Andrea H 
Abstract

UNLABELLED: 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.

Description
Keywords
Binding Sites, DNA-Binding Proteins, High-Throughput Nucleotide Sequencing, Sequence Analysis, DNA, Software
Journal Title
Bioinformatics
Conference Name
Journal ISSN
1367-4803
1367-4811
Volume Title
31
Publisher
Oxford University Press (OUP)
Sponsorship
Biotechnology and Biological Sciences Research Council (BB/L00786X/1)
Wellcome Trust (092545/Z/10/Z)
Wellcome Trust (092096/Z/10/Z)
Wellcome Trust (103792/Z/14/Z)
Cancer Research Uk (None)
We thank Charles Bradshaw for helpful comments on the software. This work was supported by the BBSRC [BB/L00786X/1] and Wellcome Trust [092545]. The Gurdon Institute is supported by core funding from the Wellcome Trust [092096] and CRUK [C6946/A14492].