How to download Protein Expression data through manifest file from TCGA ?

Question

[Muhammad Haseeb]

Hi,

I have a pretty simple question. I need to download the Protein expression data. TCGA disclose data due to maintenance, but they provide me "manifest" file. Which contains this type of information "id filename md5 size state 435c980f-85ae-4f46-bfb5-c49db03c115b nationwidechildrens.org_clinical.TCGA-33-4538.xml e56e2822ef0778f4618d4cfeb702d4c9 34188 live e521e0dd-4ef1-406e-b9b6-8224a74e3d61 " How can I download data by using "manifest" file. I will be waiting for your smart answers :) Thanks

[mforde84]

I'm pretty sure all you have to do is specify the manifest file in the gdc-client, (e.g., gdc-client download -m manifest.file.txt):

usage: gdc-client download [-h] [--debug] [-v] [--log-file LOG_FILE]
                           [-t TOKEN_FILE] [-H HOST] [-P PORT] [-d DIR]
                           [-s server] [--no-segment-md5sums]
                           [--no-file-md5sum] [-n N_PROCESSES]
                           [--http-chunk-size HTTP_CHUNK_SIZE]
                           [--save-interval SAVE_INTERVAL]
                           [--no-related-files] [--no-annotations] [-u]
                           [-m MANIFEST]
                           [file_id [file_id ...]]

Answer 1

[Smandape]

Maybe this is too late to reply but might help someone else as well. All the TCGA's data is available via Genomic Data Commons (GDC) portal. For downloading files using a manifest file you can use their Data Transfer Tool (here). It is easy to use and their documentation mentions in detail how to download the data. Hope this helps!