Downloading CHIP-seq bed files for ENCODE Histone modification data

Question

[morovatunc]

Hi,

I would like to get Chip-seq bed files for multiple histone modifiers and cell lines. However, when I sure detailed search of Encode Chip-Seq matrix it is really hard to get bed files, because for every single file I have to copy the GSM code to omnibus and download. Since I have 71 files, is there a way to download this easier?

Any suggestion would be very good so please dont hesitate to share.

Thank you very much

Tunc

This is the link of chip-seq matrix from ENCODE.

Answer 1

[Benn]

I think you can use the ftp

Answer 2

[jerry]

Hi Tunc, If you're still trying to find an easy way to download ENCODE ChiP-Seq datasets, you can use a bioinformatics tool called BioShed (https://www.bioshed.io). It's easy to get started and the steps are as follows:

To install:

pip install bioshed

To initialize and setup (you will need an AWS account to access the ENCODE files, you can find help at https://www.bioshed.io/docs/):

bioshed init
bioshed setup aws

Then, you just need to type something like:

bioshed search encode breast cancer chip-seq
bioshed download encode --filetype BED

Hope that helps!