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BigBed track flattened up on one line #1077
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Try setting the display mode to EXPANDED
```
displayMode: 'EXPANDED'
```
By default it is set to collapsed. This will put the variants on multiple
lines, however its not going to look like the UCSC track you reference. It
looks like the display mode there is set to "FULL", which puts every
variant on a new line.
|
Thanks for your answer @jrobinso! |
If they don't overlap they will be on the same line. igv.js does not
support "FULL". Can you post a screenshot?
…On Fri, Mar 13, 2020 at 12:47 AM Chiara Rasi ***@***.***> wrote:
Thanks for your answer @jrobinso <https://github.com/jrobinso>!
I've tried to set the displayMode to EXPANDED or even FULL but the result
is exactly the same, all variants on the same line..
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Here is how the "EXPANDED" displayMode looks like in the interval: chr21:47408993-47409093 But when I read the bigBed in the same interval there are the following variants:
|
OK that does look like a problem. Could you post your track configuration below and I will look into this later today. Also, what version of igv.js are you using? |
It's very likely that I'm using some wrong parameters in the track settings! My complete track configuration looks like this:
where clinvar_snvs is https://hgdownload.soe.ucsc.edu/gbdb/hg38/bbi/clinvar/clinvarMain.bb First I was using version 2.3, then I switched to 2.4, but the visualization didn't improve. Thank you so much for the help! |
Hi @jrobinso, I was wondering if you had time to take a look at this. I totally understand if you are busy so no rush! :) |
Sorry, other things intervened. Thanks for the reminder, I will look at it
tomorrow.
…On Wed, Mar 25, 2020 at 12:22 AM Chiara Rasi ***@***.***> wrote:
Hi @jrobinso <https://github.com/jrobinso>, I was wondering if you had
time to take a look at this. I totally understand if you are busy so no
rush! :)
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Thanks! |
OK I found the problem, thanks for your patience. Bigbed files were not properly "packed" for expanded mode. Your example figure was in a region with a single long variant, which covered up the smaller variants. See the screenshot below for what it should look like. The fix will require some testing before release, I will update here when it is released. |
Thank you so much!! 🥇 |
Hi @jrobinso, we are planning to switch to the new release as soon as it's out, and in the meanwhile we've been using the nightly snapshot (http://igv.org/web/snapshot/dist/igv.js) which contains this bugfix. Today we've noticed that the reference track is strangely gone. An error or some planned change in the code? Thanks! |
Definitely not planned! I'll look into it.
…On Tue, Apr 7, 2020 at 7:34 AM Chiara Rasi ***@***.***> wrote:
Hi @jrobinso <https://github.com/jrobinso>, we are planning to switch to
the new release as soon as it's out, and in the meanwhile we've been using
the nightly snapshot (http://igv.org/web/snapshot/dist/igv.js) which
contains this bugfix.
Today we've noticed that the reference track is strangely gone. An error
or some planned change in the code?
Thanks!
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I think this is resolved, if not re-open a new issue this was has multiple topics. |
Yes, it works perfectly now, thanks!!! |
Hello and thanks for the amazing software, we are using it in our repo and our alignments look great!
Some days ago I decided to try to load the bigbed tracks that UCSC is providing as clinvar tracks (http://hgdownload.soe.ucsc.edu/gbdb/hg19/bbi/clinvar/) and I got weird results, see this issue for reference: Clinical-Genomics/scout#1793
Looks like all the variants are displayed on a single line.
This is the track description in UCSC: http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=800793167_hrmbHk3PnFAEufLOaCuuAKssHaP4&c=chr21&g=clinvar
Is it a matter of wrong settings I'm using or the files are not completely supported?
My settings look like this:
Thanks for your help!
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