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Bong-Hyun Kim

Publications and source records attributed to Bong-Hyun Kim.

2 recordsLinked to original sources
bioRxiv2015

ME-plot: A QC package for bisulfite sequencing reads

Summary: Bisulfite sequencing is the gold standard method for analyzing methylomes. However, the effect of quality control in bisulfite sequencing has not been studied extensively. We developed a package ME-Plot to detect the errors in bisulfite sequencing mapping data and produce higher quality methylation calls by trimming low quality portions of the reads. Our simulation results on both randomly generated reads where methylation status is known and real world data indicate that ME-plot can detect errors in methylation mapping procedures and suggest post-processing steps to reduce the errors. ME-Plot requires SAM/BAM files for its analysis. Availability: The python package is available at the following URL. https://github.com/joshuabhk/methylsuite

Bioinformatics↗
bioRxiv2015

Factorbook Motif Pipeline: A de novo motif discovery and filtering web server for ChIP-seq peaks

SummaryHigh-throughput sequencing technologies such as ChIP-seq have deepened our understanding in many biological processes. De novo motif search is one of the key downstream computational analysis following the ChIP-seq experiments and several algorithms have been proposed for this purpose. However, most web-based systems do not perform independent filtering or enrichment analyses to ensure the quality of the discovered motifs. Here, we developed a web server Factorbook Motif Pipeline based on an algorithm used in analyzing ENCODE consortium ChIP-seq datasets. It performs comprehensive analysis on the set of peaks detected from a ChIP-seq experiments: (i) de novo motif discovery; (ii) independent composition and bias analyses and (iii) matching to the annotated motifs. The statistical tests employed in our pipeline provide a reliable measure of confidence as to how significant are the motifs reported in the discovery step.\n\nAvailabilityFactorbook Motif Pipeline source code is accessible through the following URL. https://github.com/joshuabhk/factorbook-motif-pipeline

Bioinformatics↗