Download tsv problem help?

[Aslan, Deniz]

Hello,

 

I am trying to download a TP53 query:

https://www.cbioportal.org/results/mutations?plots_horz_selection=%7B%7D&plots_vert_selection=%7B%7D&plots_coloring_selection=%7B%7D&mutations_gene=AKT1&tab_index=tab_visualize&Action=Submit&session_id=68befe74f9eac4817fed16d6

 

Has over 20000 samples and tsv will not download, could you help?

 

Thank you very much!

 

 

Deniz Aslan

Staff Pathologist

Minneapolis VAHCS

612 467 2508

 

[Tim Kuijpers]

Dear Deniz,

I believe you are running into the limitations of downloading large files via the browser (which is a know issue that is tracked here: https://github.com/cBioPortal/icebox/issues/557). Due to the large sample size and the number of mutations, it appears that the browser runs out of memory (I attempted to download the mutations table from your query).

I can think of two approaches that might help:
1) Create sub selections of your studies and download the mutation table in batches. It looks like downloading the mutation table succeeds when there are 10000 patients. 

2) You can get all the mutation data from DataHub by looking for the data_mutations_extended.txt files in each study folder here:  https://github.com/cBioPortal/datahub/tree/master/public. Note that the OncoKB annotations are missing, as they are retrieved in real-time. You can annotate them yourself by using the OncoKB annotator tool. 

I  hope this helps! If you have any further questions, please hit reply all, so our continued conversation is captured by the cBioPortal Google groups.

Best,

Tim