SraTailor
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SraTailor is a simple GUI software for visualizing published ChIP-seq raw data (Video 1).
Main function of SraTailor is to convert SRAs into BigWig files.
SRAs: High-throughput sequence raw data deposited in public databases.
BigWig: Suitable format for graphically visualizing with genome browser.
Much simple usage is one of the most remarkable features of SraTailor. For example, SraTailor makes BigWig file only by entering an accession number of SRA of published ChIP-seq data. Resultant BigWig file allows you to view the protein occupancy at the genomic position of interest (Video 2). Setup of SraTailor is much easy and simple (Video 3).
As input, SraTailor also accepts your Fastq files, which are the raw sequence data produced by your own sequencing experiments (Video 5). SraTailor produces not only BigWig files but, optionally, also BAM and peak-call BED files. Also available is to process with command-line-like optional settings (Video 4).
SraTailor is a free software and runs on Mac, Windows, and Ubuntu!
NOTE!! (September 23, 2016)
How to run SraTailor on macOS Sierra? (see PDF instruction)
Video Introduction
(1) What is SraTailor? (►01:22)
(2) Basic Usage (►02:06)
(3) Preparation of genome libraries (►00:29)
(4) Advanced usage (►02:11)
(5) My files as input (►00:48)
References
1) Oki et al. (2014). SraTailor: Graphical user interface software for processing and visualizing ChIP-seq data. Genes Cells. Link
2) 沖 真弥 (2014) SraTailor: 誰でも使えるChIP-seqデータの可視化ツール. 実験医学 (in Japanese) Link
News!
November 11, 2017
SraTailor ver 1.0.7 is now available. (Download; ChangeLog)
To update your SraTailor, see here.
December 06, 2015
ChIP-Atlas: comprehensive and integrative database for almost all published ChIP-seq data is opened.
Cited by
Munehira Y, et al. Systematic analysis of known and candidate lysine demethylases in the regulation of myoblast differentiation. J Mol Biol. 2016. PMID: 27732873.
Fujita K, et al. CHD7, Oct3/4, Sox2, and Nanog control FoxD3 expression during mouse neural crest-derived stem cell formation. FEBS J. 2016. PMID: 27579714.
Fujikawa D, et al. Polycomb-dependent epigenetic landscape in adult T-cell leukemia. Blood. 2016. PMID: 26773042.
Okamoto R, et al. Sixteen additional enhancers associated with the chicken Sox2 locus outside the central 50-kb region. Dev Growth Differ. 2015. PMID: 25431100.
Bengtsen M, et al. c-Myb Binding Sites in Haematopoietic Chromatin Landscapes. PLoS One. 2015. PMID: 26208222.