Issue to show eCLIP information

[Eric Ho]

Hi,

I have added the ENCODE RNA Trackhub from the Trackhub to my GB.

I chose to display all eCLIP targets. See screenshot below:

But I encountered issues in the following cases:

1. When I turned on eCLIP (by biosample) for all three cell lines: adrenal gland, HepG2, and K562. Only Adrenal gland was displayed. See the screenshots below:

2. When I turned off (hide) "adrenal gland", GB showed nothing. See the screenshots below:

 

3. When I selected only K562, GB displayed HepG2 tracks for one target only, i.e., UTP18.

It is hard to describe the issues in email. Apologies for the messiness.

Your help is much appreciated.

Eric Ho

Associate Professor of Biology

Lafayette College

O: 610-3305846

URL: https://sites.lafayette.edu/hoe/

[Matthew Speir]

Hello, Eric.

Thank you for your question about eCLIP data in the UCSC Genome Browser.

The reason why the HepG2 and K562 tracks don't come up when you check the box is because the creators of that hub have not enabled any of the tracks in that collection by default.

When you're configuring the tracks as shown in your screenshot under (1), click the track title, e.g. "eCLIP (by biosample) HepG2", set the "Maximum display mode" to "Full" (or your preferred visibility mode), and then scroll down to the large table and select the data for the targets you're interested in. Once you're done, click "Submit". Repeat these steps for the K562 and adrenal gland tracks to show additional data in these biosamples as well.

I think the reason you're seeing some of the tracks turn on/off as you switch between the adrenal gland/HepG2/K562 tracks is that we have code to turn on a single subtrack when none are selected. But, it seems that it's not working as intended when you initially turned on the HepG2 and K562 tracks as no subtracks are turned on.

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.

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Matthew Speir

UCSC Genome Browser, User Support

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