bam track browser detailed info display of a single read is inoperative
Sol Katzman
Although it has been quite a while since I used the feature, I am pretty
sure that I used to be able to click on a single read from a custom bam track
display to get the full details of that read (or read-pair) based on the read ID.
But trying on the standard browser (or genome-preview), this feature seems to
be inoperative. When I click on a read (or right-click and select "Show details for <readID>")
the page that comes up says:
Custom Track <my custom track>
<my custom track description>
A link to "Go to <my custom track> track controls"
I have tried this on mm10, sacCer3 assemblies
I have tried this on FireFox and Chrome (windows 10).
I have tried this with the track in squish, pack, full modes
Here is an mm10 session that is zoomed in to a small section of one bam track,
showing 4 different read-pairs that exhibit this behavior.
https://genome.ucsc.edu/s/Solkatzman/mm10_gaplinc_az010_bam
Thanks for your attention.
Sol.
Jairo Navarro Gonzalez
Hello Sol,
Thank you for reporting your issues when loading your BAM custom track.
You have discovered a bug for paired-end BAM files, and it has been fixed on our development server. The fix will be released on Feb. 28, 2023.
Thank you again for bringing this to our attention.
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
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Sol Katzman
That's excellent! (I'm glad I hadn't missed something obvious.)
This is not critical, but will the fix be available on genome-test or genome-preview before the Feb 28, 2023 release?
Thanks again for the rapid response.
/Sol.
Luis Nassar
Hi, Sol.
The change is now available on genome preview (http://genome-preview.cse.ucsc.edu). I'm sure you are aware but we have to add the usual disclaimer that features on our preview server have not undergone QA and are subject to change at any time.
Thanks again for bringing this up, and let us know if you see anything else.
Lou Nassar
UCSC Genomics Institute
To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/493acc54-90aa-7875-56eb-10d620b691b3%40ucsc.edu.
Sol Katzman
/Sol.