https://divingintogeneticsandgenomics.com/tags/ucsc/ Recent content in UCSC on Chatomics Hugo -- gohugo.io en-us © 2018 Ming 'Tommy' Tang Thu, 22 Oct 2015 14:32:00 -0700 https://divingintogeneticsandgenomics.com/archive/cytogenetic-band-explained/ Thu, 22 Oct 2015 14:32:00 -0700 https://divingintogeneticsandgenomics.com/archive/cytogenetic-band-explained/ This is a review of the basic concept of cytoband in molecular/cell biology. See the original link by Strachan, T. and Read, A.P. 1999. Human Molecular Genetics, 2nd ed. New York: John Wiley & Sons. Each human chromosome has a short arm ("p" for "petit") and long arm ("q" for "queue"), separated by a centromere. The ends of the chromosome are called telomeres. Each chromosome arm is divided into regions, or cytogenetic bands, that can be seen using a microscope and special stains. https://divingintogeneticsandgenomics.com/archive/convert-bam-file-to-bigwig-file-and-visualize-in-ucsc-genome-browser-in-a-box/ Thu, 23 Oct 2014 13:13:00 -0700 https://divingintogeneticsandgenomics.com/archive/convert-bam-file-to-bigwig-file-and-visualize-in-ucsc-genome-browser-in-a-box/ I just came across UCSC genome browser in a box Gbib, and I want to try it out. what is Gbib? from the link above: "Genome Browser in a Box (GBiB) is a "virtual machine" of the entire UCSC Genome Browser website that is designed to run on most PCs (Windows, Mac OSX or Linux). GBiB allows you to access much of the UCSC Genome Browser's functionality from the comfort of your own computer. https://divingintogeneticsandgenomics.com/archive/liftover-wig-file/ Fri, 04 Apr 2014 14:44:00 -0700 https://divingintogeneticsandgenomics.com/archive/liftover-wig-file/ I was looking at a public ChIP-seq data set, but the author did not put the raw sequence data in the GEO database. Instead, they uploaded a wig file of the ChIP-seq signal file and it was mapped to human hg18 reference genome. All the other data sets I am analyzing are mapped to hg19, so I have to liftover this wig file to hg19 also. Solution: CrossMap! http://crossmap.sourceforge.net/ 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/mysql-rocks/ Tue, 19 Nov 2013 17:18:00 -0800 https://divingintogeneticsandgenomics.com/archive/mysql-rocks/ I just finished the first chapter of MySQL by Paul DuBois http://www.amazon.com/MySQL-5th-Edition-Developers-Library-ebook/dp/B00C2SFK2Q I was really excited to explore the power of mysql. Just by following the command examples of the two sample databases in the book, I learned a lot. I am studying biology, so, I want to make practical use of mysql. One of the databases on top of my mind is the UCSC genome browser database http://genome.ucsc.edu/goldenPath/help/mysql.html connect to the database: https://divingintogeneticsandgenomics.com/archive/ucsc-genome-browser-tutorial/ Thu, 01 Aug 2013 11:56:00 -0700 https://divingintogeneticsandgenomics.com/archive/ucsc-genome-browser-tutorial/ see here openhelix http://www.openhelix.com/cgi/tutorialInfo.cgi?id=76 I use UCSC genome browser so much, but I did not realize that it has much more functions I've missed before watching the video. Related tutorials This tutorial is a part of the tutorial group UCSC Tutorials. You might find the other tutorials in the group interesting: ENCODE Foundations: ENCyclopedia of DNA Elements UCSC Genome Browser: An Introduction: The UCSC Genome Browser Introduction UCSC Genome Browser: Custom Tracks and Table Browser: UCSC Genome Browser advanced topics UCSC Archaeal Genome Browser: Provides you with many research and analysis tools that can be used to examine the genomes of more than 50 microbial species from the domain archaea. https://divingintogeneticsandgenomics.com/archive/download-data-from-ucsc-database-to-local-drive/ Sat, 30 Mar 2013 16:13:00 -0700 https://divingintogeneticsandgenomics.com/archive/download-data-from-ucsc-database-to-local-drive/ I wanted to download UCSC refGene table to my local computer. http://genome.ucsc.edu/goldenPath/help/mysql.html However, it looks like it is not possible to direct pull data from UCSC to a local host Database. on linux command line, mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A SHOW Databases; USE hg19; SHOW tables like "%ref%"; +------------------------+ | Tables_in_hg19 (%ref%) | +------------------------+ | kgXref | | kgXrefOld5 | | refFlat | | refGene | | refLink | | refSeqAli | | refSeqStatus | | refSeqSummary | +------------------------+ 8 rows in set (1.