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cBioPortal / cbioportal

cBioPortal for Cancer Genomics
https://cbioportal.org
GNU Affero General Public License v3.0
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Cytobands not shown #10546

Closed berguner closed 9 months ago

berguner commented 10 months ago

Hi,

We have an internal cBioPortal (5.4.7) that we initialized using the latest Docker compose recipe and seed-cbioportal_hg19_hg38_v2.13.1.sql.gz seed DB. I followed the guide for creating the CNA data in DISCRETE_LONG. The study gets imported without any error and I can see the CNA values in the sample view but the Cytoband field is empty.

Meta file contents:

cancer_study_identifier: TEST-STUDY
genetic_alteration_type: COPY_NUMBER_ALTERATION
datatype: DISCRETE_LONG
stable_id: cna
show_profile_in_analysis_tab: true
profile_name: Copy number estimations
profile_description: Putative copy-number from ASCAT Values: -2 = homozygous deletion; -1 = hemizygous deletion; 0 = neutral / no change; 1 = gain; 2 = high level amplification.
data_filename: data_discrete_cna.txt

Head of data file:

Hugo_Symbol Entrez_Gene_Id  Sample_Id   Cytoband    Value
A1BG    1   WES_25  19q13.43    0
A1BG    1   WES_9   19q13.43    1
A1BG    1   WES_8   19q13.43    0
A1CF    29974   WES_25  10q11.23    0
A1CF    29974   WES_9   10q11.23    0
A1CF    29974   WES_8   10q11.23    0

Can you please help me figure out solving this issue? Which tables are relevant in the DB?

Best, Bekir

berguner commented 9 months ago

Using the latest seedDB seems to solve the problem.