Scale on the y axis of the signal landscape

[Ngubo,Mzwanele]

Hi,

I would like to find out as to what is the scale on the y axis of the signal landscape mean? Is it the number of tags/spots?

Thanks,

Mzwanele

The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.

[Matthew Speir]

Hi Mzwanele,

Thank you for your question about what the y-axis represents in the UCSC Genome Browser.

What the y-axis represents will depend on what track and type of data that you are looking at. You find can the information about the display conventions for most tracks on their "description page". You can get to the description page by either clicking the gray bar next to the track in main Genome Browser image or by finding the track in one of the various track groups below this image and clicking the track name.

For example, for the "wiggle" graph tracks from the "GIS RNA PET" track, the y-axis represents the base-by-base density of tags on the different strands as mentioned on its description page: https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeGisRnaPet. On the other hand, for the phyloP Conservation "wiggle" graph track, it represents the base-by-base scores determined by the phyloP program as described on its track description page: https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=cons100way (scroll down to the "PhyloP Conservation" section).

If you can provide us with the organism (e.g. human), UCSC assembly name (e.g. hg19 or hg38), and the name of the track you are working with, we may be able to point you in the right direction of the description page where you can find this information.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Matthew Speir
UCSC Genome Bioinformatics Group

--