Dataset Information

Damidseq_pipeline: an automated pipeline for processing DamID sequencing datasets.

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.

SUBMITTER: Marshall OJ

PROVIDER: S-EPMC4595905 | biostudies-literature | 2015 Oct

REPOSITORIES: biostudies-literature

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Publications

damidseq_pipeline: an automated pipeline for processing DamID sequencing datasets.

Marshall Owen J OJ Brand Andrea H AH

Bioinformatics (Oxford, England) 20150625 20

<h4>Unlabelled</h4>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 da ...[more]

PMID: 26112292

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