maximilianh
commented
5 years ago Yes, this is because there is
geneIdType='symbols'
In your cellbrowser.conf file. It should be 'auto' to get the auto-translation.
Oops. the default was symbol/gencode-human! I chose a stupid default. Changed it now. Thanks!
Release 0.4.49 (committed a ton of other code for the MS update, will email around later on that)
On Fri, Mar 8, 2019 at 6:20 PM Matt Speir notifications@github.com wrote:
For some reason, I can't search by gene symbol in my cell browser: https://genome-test.gi.ucsc.edu/~mspeir/cb_pancreas_csv_v4/?ds=HCA_Pancreas_Aging
Data for this browser is in: /hive/users/mspeir/cellbrowserTest/pancreas/new_metadata_test/matrix_files/cbScanpyOut_pancreas_aging
Do you know why? In the docs, you say "ENSG and ENSMUSG gene identifiers will be translated automatically to symbols." (https://cellbrowser.readthedocs.io/tabsep.html?highlight=gene%20symbol), but that doesn't seem to be happening here. It tried it on datasets that have ENSG* IDs with version numbers and those without and it doesn't seem to work in either case.
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matthewspeir
For some reason, I can't search by gene symbol in my cell browser: https://genome-test.gi.ucsc.edu/~mspeir/cb_pancreas_csv_v4/?ds=HCA_Pancreas_Aging
Data for this browser is in: /hive/users/mspeir/cellbrowserTest/pancreas/new_metadata_test/matrix_files/cbScanpyOut_pancreas_aging
Do you know why? In the docs, you say "ENSG and ENSMUSG gene identifiers will be translated automatically to symbols." (https://cellbrowser.readthedocs.io/tabsep.html?highlight=gene%20symbol), but that doesn't seem to be happening here. It tried it on datasets that have ENSG* IDs with version numbers and those without and it doesn't seem to work in either case.