RNA Seq HTSeq download GDC portal

Question

[Rob]

Hi friends,

I am trying to download ht-seq file form GDC portal but it gives me one file for each patients. Can you please let me know how to download one file including all patients together for all 60000 genes?

Is there any R code for this?

Thank you

[Zhenyu Zhang]

Btw, HTSeq workflow is no longer supported in the GDC. You probably want to transit to STAR Count now

Answer 1

[DareDevil]

You can use:

xenabrowser

or

r package TCGAbiolinks

[Rob]

Thank you dare_devil

Answer 2

[Zhenyu Zhang]

Whatever method you tried, internally it stills need to download all files, before the RNA API is in production.

There are some R tools doing that, or you can use "GDC RNA tool" listed here https://gdc.cancer.gov/access-data/gdc-community-tools for aggregation

[Rob]

thanks Zhenyu Zhang