Simple bed

Consider using Hammock format for more flexibility.

Small bed files

• assume we have a bed file test.bed with following contents:
• Note: please make sure your bed files are 6 column , otherwise they won't work. Thank you!

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

bgzip test.bed

• 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