Querying ENCODE for Cell-types with certain assays available?
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20 months ago
hivemind ▴ 10

Hey everyone,

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!

ENCODE API Query • 429 views
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Yes, but unfortunately I don't have any experience with REST APIs. I understand how to send simple search requests, but I don't know how to filter for multiple conditions.

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Sure, you can use the matrix search: https://www.encodeproject.org/matrix/?type=Experiment&status=released&biosample_ontology.classification=cell+line

This lists the experiments per cell line.

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I'm not sure if this helps me. I don't want the whole Matrix, but a filtered version of it.

Please correct me if I am wrong, but if I use multiple filter options in the web interface, I get results that fulfil one condition OR the other condition? What I want is a filtered matrix that fulfils one condition AND the other condition.

I hope I make sense.

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