How do I properly visualize ATAC seq data on UCSC browser
1
1
Entering edit mode
13 months ago
rb56 ▴ 30

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?enter image description here

peaks UCSC ATAC_seq • 1.1k views
ADD COMMENT
3
Entering edit mode
13 months ago

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.

ADD COMMENT
0
Entering edit mode

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

enter image description here

ADD REPLY
1
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

Thanks a lot Alex for your wonderful help.

ADD REPLY

Login before adding your answer.

Traffic: 1870 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6