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velopipe

Velopipe is a RNA Vecocity pipeline for SEQC.

Setup

The pipeline is a part of SCING (Single-Cell pIpeliNe Garden; pronounced as "sing" /siŋ/). For setup, please refer to this page. All the instructions below is given under the assumption that you have already configured SCING in your environment.

Create Job Files

You need two files to compute RNA velocity - one inputs file and one labels file. Use the following example files to help you create your configuration file:

  • config/template.inputs.json
  • config/template.labels.json

For more information, please refer to this page:

Submit Your Job

conda activate scing

./submit.sh \
    -k ~/keys/cromwell-secrets.json \
    -i config/your-sample.inputs.json \
    -l config/your-sample.labels.json \
    -o Velopipe.options.aws.json

\