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Starting a new assay or project

Whenever you obtain sequencing data from Genomic's Platform, you have to create an Assay. By running the commands below, you will have option to fill all required information about the experiment. This workflow will help us with tracking of all sequencing done in our lab.

Assay

module load miniconda/latest
source activate brickman

cd /home/$USER/Brickman/assays
cruft create https://github.com/brickmanlab/ngs-template --directory="assay"

Next, please copy all fastq files from CPR share to folder data/raw/fastq. All processed data from a pipeline should be copied to data/processed folder.

rsync -avzh --progress --chmod=2775 ~/ucph/ndir/SUN-CPR-genomics_data/... <ASSAY_ID>/raw/fastq

After copying all the files, please run the last command.

chmod -R 775 /maps/projects/dan1/data/Brickman/assays/<ASSAY_ID>

Project

Every time you want to make some analysis, you should create a project. Our folder structure will allow you to easily link various experiments to your project and make your analysis easier.

Please use the following naming convention: surname-<YOUR_CODENAME>

module load miniconda/latest
source activate brickman

cd /home/$USER/Brickman/projects
cruft create https://github.com/brickmanlab/ngs-template --directory="project"

Link required assays to your project.

ln -s /maps/projects/dan1/data/Brickman/assays/<ASSAY_ID> /maps/projects/dan1/data/Brickman/projects/<PROJECT_ID>/data/assays/

Link external data if needed

ln -s /maps/projects/dan1/data/Brickman/shared /maps/projects/dan1/data/Brickman/projects/<PROJECT_ID>/data/external/