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- Title
damidseq_pipeline: an automated pipeline for processing DamID sequencing datasets.
- Authors
Marshall, Owen J.; Brand, Andrea H.
- Abstract
Summary: 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).
- Subjects
NUCLEOTIDE sequencing; DNA-binding proteins; UNIX operating systems; ADENINE; METHYLATION
- Publication
Bioinformatics, 2015, Vol 31, Issue 20, p3371
- ISSN
1367-4803
- Publication type
Article
- DOI
10.1093/bioinformatics/btv386