I'm currently working on a small project where I want to investigate how much certain assay types are overlapping. For this I want to use data from the ENCODE website.
The question is, if it is possible to query the ENCODE data for cell-lines where a certain number of assays is present. For example all cell-lines that have both DNase-seq and ATAC-seq, or WGBS data and ChIP-seq data.
EDIT: I want to automatically create a list of files that fulfill the requirements and download the files. Everything else should be excluded.
I tried working with the REST API of ENCODE, but I don't understand how to use it properly.
Help would be very much appreciated!