How to visualize published ChIP-seq raw data. Center for Developmental Biology

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Past Events

Category	Seminar
Date and Time	2014-07-23 16:00 - 17:00
Venue	Seminar Room A7F
Speaker	Shinya Oki
Affiliation	Department of developmental Biology, Graduate School of Medical Sciences, Kyushu University
Title	How to visualize published ChIP-seq raw data.
Poster	click here to download(PDF)
Host	Go Shioi
Summary	Background: ChIP-seq is a powerful method for comprehensively knowing the genomic regions occupied by proteins such as transcription factors and modified histones. Raw sequence data of published ChIP-seq experiments are all deposited in public databases and are publically available to every researcher. However, in order to visualize the ChIP-seq data of interest on genome browser, the corresponding raw sequence data must be downloaded and converted into a BigWig-formatted file through complicated command-line processing. Such hurdles hamper a wide range of biologists from exploiting the publically available ChIP-seq data. Project 1: I developed a Mac GUI software package, SraTailor, which automatically converts ChIP-seq raw data into a BigWig-formatted file. Simplicity of use is one of the most notable features: entering an accession number of published ChIP-seq raw data and clicking the mouse are the only steps to graphically visualize the data on genome browser. Optionally, SraTailor is able to make peak calls, and also to process “your” ChIP-seq raw data as input. SraTailor is freely available at: http://www.devbio.med.kyushu-u.ac.jp/sra_tailor Project 2 (Ongoing): I am constructing a database to visualize all published ChIP-seq results on genome browser. You will be able to graphically know how much and which proteins are verified to bind to a genomic region of your interest.