Question: Link to TCGA mutation calling benchmark dead?
0
gravatar for hoseintoossi
2.8 years ago by
hoseintoossi40
Iran/Tehran
hoseintoossi40 wrote:

I cant find the TCGA variant calling benchmark 4 at https://cghub.ucsc.edu/datasets/benchmark_download. Are the files still on cghub? where can I find the benchmark data?

genome • 1.3k views
ADD COMMENTlink modified 2.6 years ago by Bill Wysocki100 • written 2.8 years ago by hoseintoossi40

If you checked the program name in CGHub manifest, what are those files labelled? I am pretty sure all live TCGA data are in GDC legacy portal now. If they are not program "TCGA", GDC may have either back them up somewhere, or haven't imported them at all. I don't think you can get them easily.

ADD REPLYlink written 2.7 years ago by Zhenyu Zhang240
1
gravatar for Bill Wysocki
2.6 years ago by
Bill Wysocki100
USA / Chicago / GDC - CDIS - UChicago
Bill Wysocki100 wrote:

You probably have worked this out already, but I'll post this for others:

Instructions on downloading the Benchmark 4 files can be found here: https://gdc.cancer.gov/resources-tcga-users/tcga-mutation-calling-benchmark-4-files

Downloading the files with the manifest requires the GDC Data Transfer Tool. It can be downloaded/ installed here: https://gdc.cancer.gov/access-data/gdc-data-transfer-tool and documentation is available here: https://gdc-docs.nci.nih.gov/Data_Transfer_Tool/Users_Guide/Getting_Started/

Best,

-Bill - GDC User Services Team

ADD COMMENTlink written 2.6 years ago by Bill Wysocki100
0
gravatar for Jordan Anaya
2.8 years ago by
Jordan Anaya950
US/Charlottesville
Jordan Anaya950 wrote:

They moved everything to the GDC: https://gdc.nci.nih.gov/, not sure if you'll be able to find what you're looking for.

ADD COMMENTlink written 2.8 years ago by Jordan Anaya950

Did you manage to find them? I used these data in a workshop recently and wanted to give the link to where to download the data, only to find they had disappeared!

ADD REPLYlink written 2.8 years ago by mark.dunning200

I have no idea how to find previous TCGA files on the GDC portal.

ADD REPLYlink written 2.8 years ago by Jordan Anaya950

https://gdc-portal.nci.nih.gov/legacy-archive/search/f

ADD REPLYlink written 2.7 years ago by Zhenyu Zhang240
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 714 users visited in the last hour