Learn about the Browser: Difference between revisions

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** Some explanations how to read the makeDb files: [http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/hg/doc/bashVsCsh.txt bashVsCsh]  
** Some explanations how to read the makeDb files: [http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/hg/doc/bashVsCsh.txt bashVsCsh]  
** [[Implementation_Notes|Notes on the history of the internal tools: Autosql. Blastz. Chains and nets]]
** [[Implementation_Notes|Notes on the history of the internal tools: Autosql. Blastz. Chains and nets]]
* Whole-genome multiple alignments
* Whole-genome multiple alignments ([[Chains and Nets]])
** [[Mm9_multiple_alignment]]
** [[Mm9_multiple_alignment]]
** Whole-genome alignment pipeline: [[Chains_Nets|Angies mental model]] and [[Whole genome alignment howto|Max's howto]]
** [http://genome.ucsc.edu/FAQ/FAQlicense#license4 How to create a browser for a new genome from scratch]


== Statistics, overviews ==
== Statistics, overviews ==

Revision as of 09:56, 8 December 2009

Documentation is still somewhat dispersed. Here are some starting points:

Use the browser website

Access the data of the genome browser and process them on your machine

  • Be aware that internal coordinates (not website) are 0-based!
  • Unlike Gbrowse and Ensembl, UCSC is storing the data partially in SQL (coordiantes, outline of x-y-plots) and partially in flat text files (sequences, alignments, details of x-y-plots)
  • Table Browser: The easiest way to access data (you don't have to care whether data is stored in MySQL or in textfiles):
  • SQL-stored data (FAQ):
  • Flat-file data: Download from the ftp server (stored in /gbdb on browser servers)

Install a copy of the browser on your own machine (Unix or Mac)

Modify your own copy of the browser

Compile the source tree to get your own genomics pipeline started

Making Of: How the UCSC genome annotations are created

Statistics, overviews