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chip_utilities

README.md

ENCODE ChIP-seq utilities

Creating formatted mapping and IDR reports in Google Sheets (must use Python 2)

  1. Install dependencies:
pip install pygsheets
pip install pandas

  1. Ask for ENCODE account credentials and client_secret file (client_secret_xxxx.json) allowing scripts to use Google API.

  2. Authorize scripts to access Google Drive/Sheets for particular account:

import pygsheets

gc = pygsheets.authorize(outh_file='client_secret_xxxx.json')

# Follow OAuth procedure.

Drop resulting sheets.googleapis.com-python.json in home folder (or specify path with --apikey argument).

  1. Run mapping and IDR report:
$ python mapping_report.py --key www --assembly GRCh38 --create_google_sheet
$ python idr_report_experiments.py --all --key www --assembly GRCh38 --create_google_sheet

Note --released, which only shows results for released experiments, will bypass need for --key and DNAnexus credentials.

  1. Examine results posted to Google Sheets.