D-peaks: A visual tool to display ChIP-seq peaks along the genome
نویسندگان
چکیده
منابع مشابه
D-peaks: A visual tool to display ChIP-seq peaks along the genome
ChIP-sequencing is a method of choice to localize the positions of protein binding sites on DNA on a whole genomic scale. The deciphering of the sequencing data produced by this novel technique is challenging and it is achieved by their rigorous interpretation using dedicated tools and adapted visualization programs. Here, we present a bioinformatics tool (D-peaks) that adds several possibiliti...
متن کاملUsing combined evidence from replicates to evaluate ChIP-seq peaks
MOTIVATION Chromatin Immunoprecipitation followed by sequencing (ChIP-seq) detects genome-wide DNA-protein interactions and chromatin modifications, returning enriched regions (ERs), usually associated with a significance score. Moderately significant interactions can correspond to true, weak interactions, or to false positives; replicates of a ChIP-seq experiment can provide co-localised evide...
متن کاملFunChIP : A Functional Data Analysis approach to cluster ChIP-Seq peaks according to their shapes
4 The k-mean alignment algorithm and the cluster_peak method 9 4.1 Definition of weight in the distance function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 4.2 The cluster_peak method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13 4.3 The choice of the final classification with the bending index and the Silhouette plot . . . . . . ...
متن کاملActive promoters give rise to false positive ‘Phantom Peaks’ in ChIP-seq experiments
Chromatin immunoprecipitation (ChIP) is widely used to identify chromosomal binding sites. Chromatin proteins are cross-linked to their target sequences in living cells. The purified chromatin is sheared and the relevant protein is enriched by immunoprecipitation with specific antibodies. The co-purifying genomic DNA is then determined by massive parallel sequencing (ChIP-seq).We applied ChIP-s...
متن کاملBroadPeak: a novel algorithm for identifying broad peaks in diffuse ChIP-seq datasets
SUMMARY Although some histone modification chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) signals show abrupt peaks across narrow and specific genomic locations, others have diffuse distributions along chromosomes, and their large contiguous enrichment landscapes are better modeled as broad peaks. Here, we present BroadPeak, an algorithm for the identification o...
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ژورنال
عنوان ژورنال: Transcription
سال: 2012
ISSN: 2154-1264,2154-1272
DOI: 10.4161/trns.22457