How to crawl "Encyclopedia of DNA Elements" data

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3.9 years ago

szp770 ▴ 10

Hi, all. Now I need to download all the transcription factor 'bed' files from ENCODE website, how could I do that?

R python Web-crawl next-gen assembly • 861 views

ADD COMMENT • link 3.9 years ago by szp770 ▴ 10

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All of them? There are many hundreds, but anyway, I'd start by reading the documentation about the ENCODE API: https://www.encodeproject.org/help/rest-api/

It might be easier (if you work on human) to simply use a dedicated database which collected ENCODE data and processed them uniformly, offering easy access such as the ReMap project: http://remap.univ-amu.fr/

ADD REPLY • link 3.9 years ago by ATpoint 85k

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YES, like to download all transcription factor bed files of a certein cell line.

ADD REPLY • link 3.9 years ago by szp770 ▴ 10

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Good, read the docs please, the API should allow access but as said, ReMap would probably be easier.

ADD REPLY • link 3.9 years ago by ATpoint 85k

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Thank you so much. However, the files from ReMap are smaller and are different from those from ENCODE/

ADD REPLY • link 3.9 years ago by szp770 ▴ 10

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