|
From: Hans Vasquez-G. <hva...@un...> - 2023-05-25 00:52:44
|
Hi Colin,
Thank you for the feedback. I updated the displayId for the two tracks to be unique. Now the example data one is working. However, our test file isn't working.
Here is an excerpt from the file. I need to update the calculations for neg_log column because it isn't correct, but I think it should be still enough information to test the GWAS plugin with our own files.
chromosome base_pair_location p_value neg_log
10 82228 0.430992 2.69769
10 82636 0.333756 2.15653
10 85696 0.838472 6.89401
10 86828 0.42009 2.63081
10 88007 0.924451 8.40332
10 88058 0.924451 8.40332
10 89716 0.363215 2.30789
10 89913 0.925755 8.42859
10 91246 0.873263 7.46901
With the config.json excerpt here:
{
"type": "FeatureTrack",
"trackId": "gwas_track_parkinsons",
"name": "GWAS Parkinsons",
"category": ["Annotation"],
"assemblyNames": ["hg19"],
"adapter": {
"type": "BedTabixAdapter",
"scoreColumn": "neg_log",
"bedGzLocation": {
"uri": "GCST011038_buildGRCh37.4col.tsv.gz"
},
"index": {
"location": {
"uri": "GCST011038_buildGRCh37.4col.tsv.gz.tbi"
},
"indexType": "TBI"
}
},
"displays": [
{
"displayId": "gwas_display2",
"type": "LinearManhattanDisplay"
}
]
}
I created the index with the following command:
tabix -0 -b 2 -s 1 -S 1 -e 2 -f GCST011038_buildGRCh37.4col.tsv.gz
If you need the URL for this jbrowse2 installation for testing, I could provide it to you directly.
Thank you for the advice.
All the best,
-Hans
________________________________
From: Colin <col...@gm...>
Sent: Wednesday, May 24, 2023 3:27 PM
To: Hans Vasquez-Gross <hva...@un...>
Cc: gmod-ajax <gmo...@li...>; Jeremiah B Reyes <jr...@un...>
Subject: Re: [Gmod-ajax] Problems installing GWAS viewer plugin
[EXTERNAL EMAIL]
Hi there, the error is saying there are two tracks with the same displayId essentially, but the displayId needs to be unique, so you can change the track config to say gwas_viewer1 and gwas_viewer2 (or any random set of unique strings)
Hope that helps!
-Colin
On Wed, May 24, 2023, 3:57 PM Hans Vasquez-Gross <hva...@un...<mailto:hva...@un...>> wrote:
Hello All,
I believe I successfully configured the addition of the GWAS plugin within the config.json file. However, when I try to load the track with the example data, I get the following error:
Error: [mobx-state-tree] Cannot resolve a reference to type 'LinearManhattanDisplayConfigurationSchema' with id: 'gwas_display' unambigously, there are multiple candidates: /jbrowse/tracks/91/displays/0, /jbrowse/tracks/92/displays/0
How would I go about troubleshooting this error? Any advice would be greatly appreciated.
Thank you,
-Hans
--
[signature_998258195]
Hans Vasquez-Gross, Ph.D
Bioinformatics Scientist,
Nevada Bioinformatics Center
https://www.unr.edu/bioinformatics
hva...@un...<mailto:hva...@un...>
_______________________________________________
Gmod-ajax mailing list
Gmo...@li...<mailto:Gmo...@li...>
https://lists.sourceforge.net/lists/listinfo/gmod-ajax
This email originated outside of the University of Nevada, Reno. Do not click on links or attachments unless you recognize the sender and know the content is safe. Report suspicious emails to the Office of Information Technology (OIT) at ab...@un....
|