RE: trouble viewing bam files
Liu, Jing
Hi there,
I used to be able to successfully view bam files through cyverse.org. However, recently, the cyverse link did not seem to work: the UCSC genome browser showed only long and short labels for the file, but no reads were deplayed, in contrast, when I replaced with a different server link that hosting the same bam file, it displayed well.
I wonder if you can help me figure out what I can do to continue to use cyverse?
Here is an example that it used to work and still works
https://data.cyverse.org/dav-anon/iplant/home/jingliu352/analyses/mm10/5umchir_cas9_gfpsgrna.bam
here is an example that does not work. I uploaded the file through Cyberduck.
https://data.cyverse.org/dav-anon/iplant/home/jingliu352/analyses/hg38/SRR10303461_M74.bam
I look forward to hearing from you soon, thanks!
Best,
Jing
Jing Liu, Ph.D.
University of Southern California
Brian Lee
Dear Jing,
Thank you for using the UCSC Genome Browser and your question about having trouble viewing bam files.
It looks like at this moment the CyVerse site is having maintenance: https://cyverse.org/maintenance
They have started a cycle of using the first Tuesday of every month from 7 am - 7 pm Pacific Time to perform work. These dates will be impacted:
September 7, 2021
October 5, 2021
November 2, 2021
December 7, 2021
However, just in case after they are back online you are still having the issue, be sure that you have made the files for both the file.bam and the file.bam.bai public on the CyVerse site. In the past, I believe CyVerse had automatic software to make any file.bam and its related file.bam.bai public, and I believe it may be different now where you may have to select both files and mark them as public manually. You can see some illustrated steps of their updated system here, http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Hosting, where you may also want to read about inquiring with your institution about hosting data.
Thank you again for your inquiry and for using the UCSC Genome
Browser. If you have any further public questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly accessible
forum. If your question includes sensitive data, you may send it
instead to genom...@soe.ucsc.edu.
All the best,
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