Correction: A Comparison of Peak Callers Used for DNase-Seq Data
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A Comparison of Peak Callers Used for DNase-Seq Data
Genome-wide profiling of open chromatin regions using DNase I and high-throughput sequencing (DNase-seq) is an increasingly popular approach for finding and studying regulatory elements. A variety of algorithms have been developed to identify regions of open chromatin from raw sequence-tag data, which has motivated us to assess and compare their performance. In this study, four published, publi...
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DNase I is an enzyme preferentially cleaving DNA in highly accessible regions. Recently, Next-Generation Sequencing has been applied to DNase I assays (DNase-seq) to obtain genome-wide maps of these accessible chromatin regions. With high-depth sequencing, DNase I cleavage sites can be identified with base-pair resolution, revealing the presence of protected regions ("footprints"), correspondin...
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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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CLIP-seq experiments are currently the most important means for determining the binding sites of RNA binding proteins on a genome-wide level. The computational analysis can be divided into three steps. In the first pre-processing stage, raw reads have to be trimmed and mapped to the genome. This step has to be specifically adapted for each CLIP-seq protocol. The next step is peak calling, which...
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GTRD-Gene Transcription Regulation Database (http://gtrd.biouml.org)-is a database of transcription factor binding sites (TFBSs) identified by ChIP-seq experiments for human and mouse. Raw ChIP-seq data were obtained from ENCODE and SRA and uniformly processed: (i) reads were aligned using Bowtie2; (ii) ChIP-seq peaks were called using peak callers MACS, SISSRs, GEM and PICS; (iii) peaks for th...
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