Simple bed

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Revision as of 09:57, 8 September 2017 by Dli (Talk | contribs)

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Consider using Hammock format for more flexibility.

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'

Submit bed 1.png

  • will bring to the default interface of browser

Submit bed 2.png

  • Click Apps -> File Upload

Submit bed 3.png

  • brings the File Upload panel

Submit bed 4.png

  • Click Choose files, select the file test.bed in your computer, after submit, the panel will look like:

Submit bed 5.png

  • Click Setup button, select format as 'BED', the click 'add as Track' button

Submit bed 6.png

  • added successfully, close this panel

Submit bed 7.png

  • 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.
  • 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
  • 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

Submit bed 10.png

  • Click Add new tracks

Submit bed 11.png

  • in the new panel, select BED

Submit bed 12.png

  • use the URL mentioned before here, and specify a name, choose the display mode optionally

Submit bed 13.png

  • click submit button, make sure you see green done message in the right corner

Submit bed 14.png

  • Close the track submission panel, jump to the regions your bed file contains, you will see the track

Submit bed 15.png