Hello again, UCSC has several standard file types - a BED file is one of them. A BED4 file is our way of saying that the BED file has 4 data columns. BED files are required to have at least 3 data columns but can vary after that. The link I sent about the data type explains each column.
To view your data in the browser, it needs to be in a file type that can be used by Custom tracks. A BED file is one option. An example can be created using your rs number: chrom chromStart chromEnd name chr3 8804370 8804371 rs53576 For the "name" value in column 4, instead of the rs number (or in addition to, with no spaces) you can add in other values. The SNP base itself or any other text. After the file is created, add in browser and track lines and load as a custom track, passing through the target assembly's gateway page using the "add custom tracks" button. The details are in my first email's link to Custom track help. Once the data is loaded as a custom track, you will be able to view it along with the native browser annotation aligned to the reference genome. I hope this information is helpful. Please feel free to contact the help mailing list again if you require further assistance or if we have misunderstood your question (perhaps send a data example?). Best regards, Jen UCSC Genome Browser Support http://genome.ucsc.edu/contacts.html [email protected] [email protected] On 6/10/10 12:41 PM, Jonathan Kim wrote: > What do you mean BED4 file. Can you give me an example using the > information I've provided you? Thank you. > > On Wed, Jun 9, 2010 at 5:03 PM, Jennifer Jackson <[email protected] > <mailto:[email protected]>> wrote: > > Hello, > > The general idea is to load data that is mapped to one of the > genomes in the Browser in a format accepted by the Custom track > submission page. > > The track dbSNP snp131 has rs53576 at chr3, base 8804121, when using > hg19. Maybe create a simple BED4 file that contains a line for each > variant for this position and put the alternate allele in the name > column (#4). > BED format: http://genome.ucsc.edu/FAQ/FAQformat.html#format1 > > To make sure that the tutorial you examined is the full version that > covers all aspects of creating and loading Custom tracks, here is > the link: > http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks > > Please feel free to write back to the list if you need more help. > > Jennifer > > --------------------------------- > Jennifer Jackson > UCSC Genome Informatics Group > http://genome.ucsc.edu/ > > > On 6/9/10 11:50 AM, Jonathan Kim wrote: > > Hello, > > I have a set of data that I want to upload to the genome > website; > however, I have no idea how I would upload my data that I have > with me. I've > read through your tutorials but it does not specifically direct > my question. > I have OXTR - rs53576 and OXTR - rs53576 which has allele's data > that > belongs to each subject that I've tested. Please get back to me > as soon as > possible. Thank you.* > * > _______________________________________________ > Genome maillist - [email protected] > <mailto:[email protected]> > https://lists.soe.ucsc.edu/mailman/listinfo/genome > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
