https://divingintogeneticsandgenomics.com/tags/bedgraph/ Recent content in Bedgraph on Chatomics Hugo -- gohugo.io en-us © 2018 Ming 'Tommy' Tang Tue, 18 Feb 2014 12:53:00 -0800 https://divingintogeneticsandgenomics.com/archive/hosting-bigwig-by-dropbox-for-ucsc-visualization/ Tue, 18 Feb 2014 12:53:00 -0800 https://divingintogeneticsandgenomics.com/archive/hosting-bigwig-by-dropbox-for-ucsc-visualization/ First, you need to get an idea of what is a bigwig file: https://genome.ucsc.edu/goldenPath/help/bigWig.html It is the binary form of wig file and allows UCSC genome browser to fetch only the data in the current window. I usually get wig file by MACS1.4 peak calling ChIP-seq data. MACS2 now does not have the -w option any more. https://github.com/taoliu/MACS/ see a discussion in the google group: https://groups.google.com/forum/#!searchin/macs-announcement/bedgraph$20ucsc$20track/macs-announcement/LBhAtmC-Zho/uZuxU8ZaqdEJ MACS2 only creates a bedgraph file http://genome. https://divingintogeneticsandgenomics.com/archive/my-first-play-with-gro-seq-data-from-sam-to-bedgraph-for-visualization/ Wed, 30 Oct 2013 18:35:00 -0700 https://divingintogeneticsandgenomics.com/archive/my-first-play-with-gro-seq-data-from-sam-to-bedgraph-for-visualization/ GRO-seq (Global run on sequencing) is a technique to capture nascent RNAs in a global manner. Different from RNA-seq which sequences the matured mRNA to infer gene expression level, GRO-seq sequences the newly generated short RNAs to infer RNApol2 binding or the production of enhancer RNAs. It was first carried out by John T.Lis at Cornell University. See their science paper in 2008: Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters