Downloading *_tcga_pan_can_atlas_2018 datasets from the github site

[Favour James]

Hi, my name is Favour
I want to contribute to NRNB for GSOC 2023. In one of our getting started tasks, we were required to download the data mutations.txt file under the datasets with the label above. However, when I'm clicking on the link provided on the github page, I'm getting the error: HTTP Status 404 – Not Found. This is the link I clicked on. Please, I humbly request help on how to download these datasets. Thank you

. 

[Benjamin Gross]

Hi Favour,

You can find all the public datasets here:

https://github.com/cBioPortal/datahub/tree/master/public

You will see folders for each of the tcga_pan_can_atlas_2018 studies.

Which folder are you having an issue downloading?

Best,

Benjamin

On Mar 21, 2023, at 2:03 PM, Favour James <favour.u...@gmail.com> wrote:

Hi, my name is Favour
I want to contribute to NRNB for GSOC 2023. In one of our getting started tasks, we were required to download the data mutations.txt file under the datasets with the label above. However, when I'm clicking on the link provided on the github page, I'm getting the error: HTTP Status 404 – Not Found. This is the link I clicked on. Please, I humbly request help on how to download these datasets. Thank you

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[Favour James]

Hi Benjamin, thanks for the response. I was having errors when i tried accessing the cBio portal website. However, I have been able to download the data using the guidelines on gitlfs. When I tried downloading it directly from the github link, it only downloaded a text document that contained the link. I also have another issue. I cannot seem to find the 'sift' columns in the *_tcga_pan_can_atlas_2018 datasets and we were required to check it. i will appreciate any guidance I can get.

[Benjamin Gross]

Hi Favour,

Ah, the files in our repository require git-lfs to download successfully.  Follow the steps found here:

https://github.com/cBioPortal/datahub#how-to-download-data

I don’t think the checked in files would be sift annotated.  Can you point me tot the NRNB page with this description?

Thanks,

Benjamin

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[Favour James]

I did not know but I later figured it out and I was successful. Thank you. This is the link:https://github.com/nrnb/GoogleSummerOfCode/issues/217. 

[Favour James]

I did not know, it was not really specified, I however figured it out later that day. 

this is it: https://github.com/nrnb/GoogleSummerOfCode/issues/217