How do I properly visualize ATAC seq data on UCSC browser

Question

[rb56]

Hi everyone,

I've tried uploading a .bedgraph and .bigWig file on UCSC Genome Browser to view the peaks. However, the data does not look like peaks, rather black bars without any height or width distribution. How can I visualize the data as peaks instead of flat bars?

Answer 1

[Alex Reynolds]

What steps did you take to upload your file? Perhaps check that you gave your track the correct type (e.g., bigWig). See: https://genome.ucsc.edu/goldenPath/help/customTrack.html#EXAMPLE1 and https://genome.ucsc.edu/goldenPath/help/customTrack.html#TRACK for example track descriptions and types.

[rb56]

Hi Alex,

Thanks for the great tip! I added the following lines at the start of my .bedgraph file and now the tracks look like this-

This might be silly, but I'm not sure I understand what the length of the vertical peaks and with of the horizontal peaks signify? Are these the number of reads assigned to a region?

Thank you very much for your help

track type=bedGraph name="BedGraph Format" description="BedGraph format" visibility=full color=200,100,0 altColor=0,100,200 priority=20

chrom chromStart chromEnd

[Alex Reynolds]

I think they generally represent enrichment of aligned read pairs. It may depend on your peak caller and parameters, how those reads are translated to signal.

[rb56]

Thanks a lot Alex for your wonderful help.