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DMRR Submission Preparation

Prepare miRNA metadata for submission to the exRNA Data Coordination Center. This project was created for the Tewari Lab at the University of Michigan.

Setup

You can download this repository with:

$ git clone https://github.com/kelly-sovacool/dmrr-submission-prep.git

Python 3 packages to install:

  • pandas
  • docopt
  • numpy
  • yaml

Usage

Create a configuration file in YAML format for your submission. Example:

group: exrna-mtewa1
user_login: sovacool
study_name: U01 Feeding Study July 2018
samples_filename: sample_sheet.csv
sample_study_names:
  - Feeding Study-30 min
  - Feeding Study-1 hr
study_id: EXR-MTEWA1FeedingStudy
working_dir: feedingStudy
templates_dir: templates
is_time_series: True
database: hg19_exrna
md5sum: daec25d670e3bb6b3ab3bbf5733df68c
fastq_filenames: HealthyControl_and_FeedingStudy_fastq_file.names.txt
tar_archive: None

The samples_filename should be the path to a csv file with the following column names: Participant.ID, Sample.ID, MT.Unique.ID, Source, and Study. Each row should be a different sample.

Run the program with:

$ dmrr_prep.py config.yaml

The program will create donors metadata, biosamples metadata, and a manifest file and write them to working_dir.