Bray GigaScience data

Download the data

• Clone the repo.

git clone https://github.com/broadinstitute/2015_Bray_GigaScience-data.git

• Install DVC and Git LFS.

• Download the files on Git LFS.

git lfs pull

• Download the profiles from S3.

dvc pull

Re-generate the data

To reproduce the profiles in this repo, run the profiling-recipe. But run the following two steps to create metadata files and fix well position names

Create metadata files

Install the conda environment in create_metadata/environment.yml and run the notebook create_metadata.ipynb to create all the metadata and platemap files.

Fix well names

Use the same conda enviroment as above and run fix_well_position.py to change the well names from a01 to A01 in the aggregated profiles. Run the recipe only after fixing the names of the wells.

Notes

quality_control step was not run because the load_data.csv.gz files did not have the column Metadata_Row. This column could be created and the quality_control step can be run later.