Contents of http://compbio.berkeley.edu/people/ornam/forHugh/:
This directory contains files to be loaded as custom tracks on the UCSC genome browser.
Each file contains the variation data of one individual's reads relative to the genome sequence. For each base where at least one read was different from the reference human genome 
assembly the browser will show entries of the sort: 84A;5C;2G, where the base appearing in the reference genome assembly appears first, followed by other variants in order of descending 
frequency (numbers indicate the number of reads each variant appeared in).
notes:
* Files ending in _ge5.txt.bz2 represent files where the most frequent non-reference variant appeared at least 5 times.
* Files ending in _BED_nf.txt.bz2 represent files where no filtration of frequency was imposed.
* The prefixes of files indicate the individuals they pertain to.

To upload a file:
1. Go to the genome browser for the human genome: http://genome.ucsc.edu/cgi-bin/hgGateway
2. Click on the 'manage custom tracks' button (just below the genome display)
3. Click on the 'Add custom track' button
4. paste the url of the track in the first text box (e.g. http://compbio.berkeley.edu/people/ornam/forHugh/ 
303N3_HCT491_varData_BED_nf.txt.bz2). If you would like to upload more than one 
track you can enter multiple url's, each on a separate line. Then, press the 'submit' button. After the browser finishes 
loading the data in the files you will be redirected to the 'manage custom tracks' page.
5.  Press the 'go to genome browser' in order to view your tracks. Your tracks should appear at the very bottom of the 
genome display window, below the SNP data. Also, they should be listed at the bottom of the page under the 'other' 
category.