View source for 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!
<pre>
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	+
</pre>
* go to browser, choose genome
* choose go to 'Genome browser'
[[File:Submit_bed_1.png]]
* will bring to the default interface of browser
[[File:Submit_bed_2.png]]
* Click Apps -> File Upload
[[File:Submit_bed_3.png]]
* brings the File Upload panel
[[File:Submit_bed_4.png]]
* Click Choose files, select the file '''test.bed''' in your computer, after submit, the panel will look like:
[[File:Submit_bed_5.png]]
* Click Setup button, select format as 'BED', the click 'add as Track' button
[[File:Submit_bed_6.png]]
* added successfully, close this panel
[[File: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.
** 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
[[File:Submit_bed_10.png]]
* Click Add new tracks
[[File:Submit_bed_11.png]]
* in the new panel, select BED
[[File:Submit_bed_12.png]]
* use the URL mentioned before here, and specify a name, choose the display mode optionally
[[File:Submit_bed_13.png]]
* click submit button, make sure you see green done message in the right corner
[[File:Submit_bed_14.png]]
* Close the track submission panel, jump to the regions your bed file contains, you will see the track
[[File:Submit_bed_15.png]]

[[Category:Tracks]]