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KMID : 0613820210310040410
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Journal of Life Science
2021 Volume.31 No. 4 p.410 ~ p.417
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ChIP-seq Library Preparation and NGS Data Analysis Using the Galaxy Platform
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Kang Yu-Jin
Kang Jin
Kim Yea-Woon
Kim Ae-Ri
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Abstract
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Next-generation sequencing (NGS) is a high-throughput technique for sequencing large numbers of DNA fragments that are prepared from a genome. This sequencing technique has been used to elucidate whole genome sequences of living organisms and to analyze complementary DNA (cDNA) or chromatin immunoprecipitated DNA (ChIPed DNA) at the genome level. After NGS, the use of proper tools is important for processing and analyzing data with reasonable parameters. However, handling large-scale sequencing data and programing for data analysis can be difficult. The Galaxy platform, a public web service system, provides many different tools for NGS data analysis, and it allows researchers to analyze their data on a web browser with no deep knowledge about bioinformatics and/or programing. In this study, we explain the procedure for preparing chromatin immunoprecipitation-sequencing (ChIP-seq) libraries and steps for analyzing ChIP-seq data using the Galaxy platform. The data analysis steps include the NGS data upload to Galaxy, quality check of the NGS data, pre- mapping processes, read mapping, the post-mapping process, peak-calling and visualization by window view, heatmaps, average profile, and correlation analysis. Analysis of our histone H3K4me1 ChIP-seq data in K562 cells shows that it correlates with public data. Thus, NGS data analysis using the Galaxy platform can provide an easy approach to bioinformatics.
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KEYWORD
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Bioinformatics, ChIP-seq, galaxy, NGS
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