Question: Download all files from encode matching filter specifications
0
gravatar for jyu429
21 months ago by
jyu429120
United States
jyu429120 wrote:

Hi, I'm wondering how I might go about downloading all the files and associated summary information from encodeproject.org that match a specific set of filters. For example, if I want

Assay: ChiP-seq

Genome assembly: GRCh38

Organism: Homo sapiens

Target of assay: histone, recombinant protein

Organ: blood, ovary

is there an easy way to download all these and the summary data at once? Thanks!

encode • 564 views
ADD COMMENTlink modified 20 months ago by Brian Gudenas90 • written 21 months ago by jyu429120
0
gravatar for Brian Gudenas
20 months ago by
United States
Brian Gudenas90 wrote:

If you go to the ENCODE project experiment matrix webpage here https://www.encodeproject.org/matrix/?type=Experiment You can select all your desired filters (Assay, Organism, data type ) then click the download button on the bottom to get a file containing the links to all desired datasets (1st line is the full sample metadata file)

To batch download everything in that file on unix you can use

xargs -n 1 curl -O -L < files.txt
ADD COMMENTlink written 20 months ago by Brian Gudenas90
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