RNA-seq study Looking for for Cancer and Virus FTP Databases

Question

[vdargisrobinson]

I'm doing an RNA-seq study and am searching for FTP databases dedicated to viruses and cancer. However, if you know of other sites more broadly related to microbiology/immunology, I would also be interested.

For cancer, so far I've found The Cancer Genome Atlas (TGCA), but I cannot cannot find a link that allows data to be transferred via FTP, the only protocol that I want to use. I started at this site: https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/

Then I clicked the Parent directory link twice on two pages, which transferred me to this error page: https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/

Further clicking does not lead me to a useful page.

Does anybody know if the TGCA supports FTP downloading?

Or if open access virus ftp databases exist?

Thanks!
-V

[Sean Davis]

Are you looking for the TCGA RNA-seq sequence data? If so, there is only one approach that you can follow and that is to apply for access to the restricted RNA-seq data. You will not find any ftp download that is "publicly available" because such a link does not exist.

[vdargisrobinson]

I am looking for TCGA RNA-seq data, as well as data from other cancer and other microbiology/immunology and cancer ftp databases.

Thanks for the info Sean. It's unfortunate there is no de-identified publicly available data from the TCGA. I'll have to look for other sources.

[vdargisrobinson]

Is RNA-seq data also restricted on the Cancer Genomics Hub?

[Sean Davis]

Yes.