Visualising BedGraph files on UCSC [custom tracks]

Question

[anu014]

Hi all!

How to add custom tracks to UCSC microbes, specifically for Mycobacterium Tuberculosis :

http://microbes.ucsc.edu/cgi-bin/hgTracks?db=mycoTube_H37RV&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr%3A10001-35000&hgsid=2721963_tz9eJcUdmBnkbQWUpERSIVCYXdeZ

Please note my file is BedGraph file which looks like this :

type=bedGraph
Chromosome      0       2       60.00000
Chromosome      2       3       61.00000
Chromosome      3       4       64.00000
Chromosome      4       5       67.00000
Chromosome      5       7       70.00000
Chromosome      7       8       71.00000
Chromosome      8       9       72.00000

If I am uploading it on above link, it's giving me this error:

Error File 'ut_broad_treat_pileup1.bdg' - Unrecognized format line 1 of file: type=bedGraph (note: chrom names are case sensitive, e.g.: correct: 'chr1', incorrect: 'Chr1', incorrect: '1')

Thank you in advance :)

[venu]

are you sure Chromosome notation is correct? Check this

Also, try to use bigwig format to view in UCSC .

Answer 1

[Arup Ghosh]

The bedGraph file you have don't use the correct formatting. A standard bedGraph file will be like the following example.

track type=bedGraph name="BedGraph Format" description="BedGraph format" visibility=full color=200,100,0 altColor=0,100,200 priority=20
chr19 49302000 49302300 -1.0
chr19 49302300 49302600 -0.75
chr19 49302600 49302900 -0.50
chr19 49302900 49303200 -0.25
chr19 49303200 49303500 0.0
chr19 49303500 49303800 0.25
chr19 49303800 49304100 0.50
chr19 49304100 49304400 0.75
chr19 49304400 49304700 1.00

For more details check: https://genome.ucsc.edu/goldenpath/help/bedgraph.html

[anu014]

Thank you for the reply.

Yes, my header & chromosome was not right. Adding correct header & changing chromosome name from 'Chromosome' to 'chr' solved my problem :

browser position chr:0-4411533
browser hide all
browser pack refGene encodeRegions
browser full altGraph
#       300 base wide bar graph, autoScale is on by default == graphing
#       limits will dynamically change to always show full range of data
#       in viewing window, priority = 20 positions this as the second graph
#       Note, zero-relative, half-open coordinate system in use for bedGraph format
track type=bedGraph name="Input" description="BedGraph format" visibility=full color=200,100,0 altColor=0,100,200 priority=20
chr     0       1       167.00000
chr     1       2       169.00000
chr     2       3       171.00000
chr     3       4       173.00000
chr     4       5       175.00000
chr     5       6       177.00000
chr     6       7       179.00000