https://divingintogeneticsandgenomics.com/tags/mysql/ Recent content in Mysql on Chatomics Hugo -- gohugo.io en-us © 2018 Ming 'Tommy' Tang Thu, 21 Nov 2013 13:05:00 -0800 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/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.