bulk download in ENCODE

Question

[Biojl]

Hi,

I'm trying to download several experiments in bulk from https://www.encodeproject.org/. I use the filters in the experiment matrix and I come up with 97 datasets. I am only interested in bed narrowPeak files (in available data), thus I select only that category. But when I click download I get only the ID of the experiments (files.txt).

When I execute the command to download by ID (xargs -n 1 curl -O -L < ../files.txt) I get hundreds of bed files instead of just the 97 files I'm interested. Any idea on how to properly do this?

Thanks in advance.

Answer 1

[Ming Tommy Tang]

try ENCODExplorer package if you use R. http://bioconductor.org/packages/release/bioc/html/ENCODExplorer.html