Mutations

[Lucas Wang]

Hello cbioportal,

I want to find the functional impact of all these mutations in the image below. Is there a way I can accomplish this without downloading each gene individually, then getting the functional impact?

Thanks,

Lucas

[Aaron L]

HI Lucas, I'm curious, are you using the api to download mutation data for this study: msk_ch_2023?
Someone has been doing so and is causing big performance problems.  If so, no worries but please stop for the time being while we work out a problem.

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[Lucas Wang]

Hello cbioportal,

Is it possible to download all mutations' functional impact (and other info) at once? For example, I don't want to download each mutation's functional impact individually. Do you guys have the function so I can download all mutations functional impact at once and not individually?

Thanks,

Lucas Wang

[Zeynep Karagöz]

Hi Lucas, 

Referring to the previous email you sent to the group, it seems this is related to the same topic. If so, please follow the guidance provided earlier:

You can download all mutation data from the Datahub and then use the OncoKB Annotator to programmatically annotate the variants. 
Please reply all to this email if you have further questions. 

Best,

Zeynep Karagöz

Product Owner & Data Engineer

E zey...@thehyve.nl

T +31 30 700 9713

W thehyve.nl

   

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[Lucas Wang]

Hello, 

So, I want to study LUAD (TCGA, GDC). I just clicked on the link for Datahub. What's the next step after I click on LUAD TCGA?

Thanks,

Lucas Wang

[Lucas Wang]

Is it possible if you provide a tutorial/video? I couldn't find any online.

[Zeynep Karagöz]

Hi Lucas, 

If you scroll down on the datahub page, you will see a file called "data_mutations.txt". You can click on the download icon at top right of this page:

This will download a MAF-like file containing all the mutations in the study you're interested in. Please take a look at this file and see if the information you're looking for is available. 

Please reply all to this email if you have further questions.

Best,

Zeynep Karagöz

Product Owner & Data Engineer

E zey...@thehyve.nl

T +31 30 700 9713

W thehyve.nl

   

[Lucas Wang]

There is no functional impact data. Is this correct?