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!
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written
by
jyu429
1 answer
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
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