Download all files from encode matching filter specifications

Question

[jyu429]

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!

Answer 1

[Brian Gudenas]

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