Shape-based peak identification for ChIP-Seq
نویسندگان
چکیده
منابع مشابه
Shape matters: Differential peak detection for Chip-seq data sets
Motivation and Objectives ChIP-Seq has rapidly become the dominant experimental technique in functional genomic and epigenomic research. Statistical analysis of ChIP-Seq data sets however remains challenging, due to the highly structured nature of the data and the paucity of replicates. Current approaches to detect differentially bound or modified genomic regions are mainly borrowed from RNA-Se...
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et al details each of these steps and discusses how peak finding tools approach the separate steps very differently (3). A follow up review by Wilbanks et al evaluated the performance of 11 ChIP-seq peak callers nearly all of which are still widely used today (4). Each step can have parameters that can be adjusted by the user, but changing these can significantly affect the final peak lists. Ca...
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UNLABELLED ChIP-seq has become a major tool for the genome-wide identification of transcription factor binding or histone modification sites. Most peak-calling algorithms require input control datasets to model the occurrence of background reads to account for local sequencing and GC bias. However, the GC-content of reads in Input-seq datasets deviates significantly from that in ChIP-seq datase...
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Sequencing data quality and peak alignment efficiency of ChIP-sequencing profiles are directly related to the reliability and reproducibility of NGS experiments. Till now, there is no tool specifically designed for optimal peak alignment estimation and quality-related genomic feature extraction for ChIP-sequencing profiles. We developed open-sourced COPAR, a user-friendly package, to statistica...
متن کاملPicking ChIP-seq peak detectors for analyzing chromatin modification experiments
Numerous algorithms have been developed to analyze ChIP-Seq data. However, the complexity of analyzing diverse patterns of ChIP-Seq signals, especially for epigenetic marks, still calls for the development of new algorithms and objective comparisons of existing methods. We developed Qeseq, an algorithm to detect regions of increased ChIP read density relative to background. Qeseq employs critic...
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ژورنال
عنوان ژورنال: BMC Bioinformatics
سال: 2011
ISSN: 1471-2105
DOI: 10.1186/1471-2105-12-15