run_encode_ATAC_pipeline

Run ENCODE ATAC pipeline on Mordor:

STEP1: Copy example json to own directory

cp /mnt/work1/users/lupiengroup/pipelines/encode-atac-pipeline-v1.9.0/example.json /path/to/directory

--OR--

cp /cluster/projects/lupiengroup/pipelines/encode-atac-pipeline-v1.9.0/example.json /path/to/directory

STEP2: Edit example json according to your own sample

STEP3: Run following command with edited json file

bash /mnt/work1/users/lupiengroup/pipelines/encode-atac-pipeline-v1.9.0/run_encode-atac-pipeline.sh edited.example.json

--OR--

bash /cluster/projects/lupiengroup/pipelines/encode-atac-pipeline-v1.9.0/run_encode-atac-pipeline.sh edited.example.json

Important things to note:

How to edit JSON:

1. https://github.com/ENCODE-DCC/atac-seq-pipeline/blob/master/docs/input_short.md
2. https://github.com/ENCODE-DCC/atac-seq-pipeline/blob/master/docs/input.md

Pipeline protocol:

https://www.encodeproject.org/atac-seq/

https://docs.google.com/document/d/1f0Cm4vRyDQDu0bMehHD7P7KOMxTOP-HiNoIvL1VcBt8/edit

Organize output:

Organize QC: