Hello,
Thank you for using the UCSC Genome Browser and sending your inquiry.
To better help debug your issues, could you send us a URL to the bigWig file you are using on the Genome Browser? If the file contains sensitive information, you can send the URL to genom...@soe.ucsc.edu or directly to me.
I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
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If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
Jairo Navarro
UCSC Genome Browser
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Hello, Jinrui.
We apologize for the delay in our response. We were able to replicate your issue and have created an internal ticket to fix the bigWigAverageOverBed output. Unfortunately, we cannot provide an estimated release date for the fix.
Thank you again for bringing this to our attention. If you would like email updates about the UCSC Genome Browser, you can subscribe to our Announcements Mailing List: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.
Gerardo Perez
UCSC Genomics Institute
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Hello, Jinrui.
We took a look at the bigWigAverageOverBed utility, and we did see the same behavior using a different dataset. This has led to some ongoing internal discussions and we haven't yet reached a consensus about it. We will try to get back to you next week.
We apologize for any inconvenience this may have caused.
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.
Gerardo Perez
UCSC Genomics Institute
Hello,
Thank you for using the UCSC Genome Browser and sending your inquiry.
For many files, mean and mean0 will be the same. For example, if the bigWig file has no undefined regions, then mean0 will be the same as the mean. This may be the case for ENCODE files, as these are coverage files, and their pipeline looks at the entire genome.
Looking at ENCFF469WVA.bigWig referenced above, it generally doesn't have missing data, so in general, mean0 should always equal mean. Most of the "missing data" is filled with zeroes, which isn't considered missing by the tool.
As an example that the tool is working as intended:
In the defined region, the mean is 1, but if you take the entire chromosome, the mean is 0.0214087.
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.
Jairo Navarro
UCSC Genome Browser
To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/CAGzk_hNtg2kQnjj2sgM42BdVsBDkHtVAvND4ByVCt7SE4hFeCw%40mail.gmail.com.