damidseq_pipeline: an automated pipeline for processing DamID sequencing datasets.
damidseq_pipeline: an automated pipeline for processing DamID sequencing datasets.
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DOI：
10.1093/bioinformatics/btv386
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发表时间：
2015-10-15
期刊：
影响因子：
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通讯作者：
Brand AH
中科院分区：
文献类型：
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作者：
Marshall OJ;Brand AH
DamID是一种用于识别DNA结合（或DNA相关）蛋白结合的基因组区域的强大技术。目前，不存在用于自动处理下一代测序DamID（DamID-seq）数据的方法，并且使用具有仅基于读段计数的归一化的DamID-seq数据集可能导致高背景和结合信号的损失。因此，DamID-seq在归一化和背景最小化方面提出了新的挑战。我们在这里描述damidseq_pipeline，这是一个软件管道，可以对多个DamID-seq FASTQ数据集执行自动归一化和背景减少。可用性和实现：开源，可从http://owenjm.github.io/damidseq_pipeline免费获得。damidseq_pipeline是用Perl实现的，与任何基于Unix的操作系统（例如Linux，Mac OSX）兼容。联系方式：o.马歇尔补充信息：补充数据可在生物信息学在线获得。gurdon.cam.ac.uk
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). Contact: o.marshall@gurdon.cam.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.