https://divingintogeneticsandgenomics.com/tags/bedtools/ Recent content in Bedtools on Chatomics Hugo -- gohugo.io en-us © 2018 Ming 'Tommy' Tang Wed, 16 May 2018 13:16:00 -0700 https://divingintogeneticsandgenomics.com/archive/get-the-peaks-that-shared-in-multiple-samples/ Wed, 16 May 2018 13:16:00 -0700 https://divingintogeneticsandgenomics.com/archive/get-the-peaks-that-shared-in-multiple-samples/ View this gist on GitHub https://divingintogeneticsandgenomics.com/archive/define-intronic-exonic-and-intergenic-regions-using-granges/ Mon, 14 Nov 2016 14:17:00 -0800 https://divingintogeneticsandgenomics.com/archive/define-intronic-exonic-and-intergenic-regions-using-granges/ You might want to use the bedtools for solutions. see Dave Tang's post. I am going to use GRanges to do exactly the same thing. However, do bear in mind that R uses 1 based coordinate system. bed files in Granges are 1 based. bedtools uses 0 based coordinate system for bed files. It could be very confusing and one can make 1 base-off mistake easily. when you have a bed file in 0 based coordinate system, if you read it into R by using import function in rtracklayer package, it will convert to 1 based internally. 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/mysql-to-get-all-the-disease-associated-snps/ Thu, 21 Nov 2013 13:05:00 -0800 https://divingintogeneticsandgenomics.com/archive/mysql-to-get-all-the-disease-associated-snps/ I want to find SNPs occur at the transcription binding sites which may potentially affect the binding of the transcription factor. I need to have a list of SNPs that are associated with diseases first. people usually go to dbSNP http://www.ncbi.nlm.nih.gov/SNP/ but the UCSC snp138 table hg19 is much better accessible in terms of parsing. See posts here: http://www.biostars.org/p/1288/ http://www.biostars.org/p/7073/ http://www.biostars.org/p/11701/ find SNPs associated with OMIM gene (by Pierre ) 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