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damidseq_pipeline: an automated pipeline for processing DamID sequencing datasets

Citation

Marshall, OJ and Brand, AH, damidseq_pipeline: an automated pipeline for processing DamID sequencing datasets, Bioinformatics, 31, (20) pp. 3371-3373. ISSN 1367-4803 (2016) [Refereed Article]

DOI: doi:10.1093/bioinformatics/btv386

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.

Item Details

Item Type:Refereed Article
Research Division:Biological Sciences
Research Group:Biochemistry and Cell Biology
Research Field:Biochemistry and Cell Biology not elsewhere classified
Objective Division:Expanding Knowledge
Objective Group:Expanding Knowledge
Objective Field:Expanding Knowledge in the Medical and Health Sciences
Author:Marshall, OJ (Dr Owen Marshall)
ID Code:108950
Year Published:2016 (online first 2015)
Web of Science® Times Cited:11
Deposited By:Menzies Institute for Medical Research
Deposited On:2016-05-12
Last Modified:2017-11-06
Downloads:0

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