How To Display Eight Samples As Ucsc Custom Tracks

Question

[Nitin]

I have 4 samples in each grp in untreated vs treated grp. I want to display all this data of two grps (8 samples) in UCSC browser. This is a methylation array data. I generated a bedgraph for one sample as -

track type=bedGraph name="A"description="A hox" visibility=full color=0,255,0                
chr2    176964720    176964720    0.018296992    
chr2    176963353    176963353    0.018508837    
chr17    46699073    46699073    0.021180405

It displays the values as bar diagram in specified color and also display the value itself. My question is How can I display all 8 tracks in different colors as well as I would like to have name of the gene (not value) to appear on the track.

Thanks

Answer 1

[Robert Sicko]

Try using standard .BED format for your track.

track name="example" description="8_samples" visibility=2 itemRgb="On"                                
chr2     176964720    176964721    gene_X-Sample1    0    +    176964720    176964721 0,255,0
chr2     176964720   176964721    gene_X-Sample2    0    +    176964720    176964721 0,255,255

Then you can change the RGB code (last value in above example) for each sample. *Note: I made the example tracks 1-bp long so there will be a tiny bar displayed in UCSC.

Answer 2

[Ian]

You might want to consider using UCSC track hubs as there are ways to group tracks together. This method requires access to a web server. Data must be provided as the "big" formats, e.g. bigBed, bigWig and so on.

[Ryan Dale]

Especially with the "multiWig" format, which overlays many bigWigs into one track: http://genome.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html#aggregate