damidseqₚipeline: an automated pipeline for processing DamID sequencing datasets

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 damidseqₚipeline, 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/damidseqₚipeline. The damidseqₚipeline 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.