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Revision as of 14:48, 18 August 2014 by Xzhou
The simple, 6-column data format is deprecated. Consider using Hammock format instead.
Small bed files
- assume we have a bed file test.bed with following contents:
chr1 13041 13106 reg1 1 + chr1 753329 753698 reg2 2 + chr1 753809 753866 reg3 3 + chr1 754018 754252 reg4 4 + chr1 754361 754414 reg5 5 + chr1 754431 754492 reg6 6 + chr1 755462 755550 reg7 7 + chr1 761040 761094 reg8 8 + chr1 787470 787560 reg9 9 + chr1 791123 791197 reg10 10 +
- go to browser, choose genome
- choose go to 'Genome browser'
- will bring to the default interface of browser
- Click Apps -> File Upload
- brings the File Upload panel
- Click Choose files, select the file test.bed in your computer, after submit, the panel will look like:
- Click Setup button, select format as 'BED', the click 'add as Track' button
- added successfully, close this panel
- Jump to the region our bed located, we will see the track
Large bed files
- For large bed files, submit an URL containing bgzip/tabix processed bed file is recommended.
- also see how to install tabix
- We still use the test.bed before as example for guide purpose.
- make sure your bed file is sorted, other bgzip/tabix won't work
- you can either use bedSort or sort command
- use bgzip to compress the test.bed file, will generate a test.bed.gz file
- use tabix to index it, will generated an additional test.bed.gz.tbi file
tabix -p bed test.bed.gz
- you have test.bed.gz and test.bed.gz.tbi now, put both file in an web location, here is my url: http://cgs.wustl.edu/~dli/
- next, using this URL http://cgs.wustl.edu/~dli/test.bed.gz for submission
- open the browser, select assembly, say hg19, click go to 'Genome browser', will bring you to the default interface of browser
- Click Tracks -> Custom tracks
- Click Add new tracks
- in the new panel, select BED
- use the URL mentioned before here, and specify a name, choose the display mode optionally
- click submit button, make sure you see green done message in the right corner
- Close the track submission panel, jump to the regions your bed file contains, you will see the track