SEQC Ada (AutomateD Analysis)
Ada is considered to be the first computer programmer and her method has been called the world's first computer program.
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.
You need two files for processing a sample - one inputs file and one labels file. Use the following example files to help you create your configuration file:
configs/template.inputs.jsonconfigs/template.labels.json
| Type | SeqcAda.assay |
|---|---|
| 10x v2 Kit | ten_x_v2 |
| 10x v3 Kit | ten_x_v3 |
| 10x NextGEM | ten_x_v3 |
Use one of the URLs below for the reference genome:
| Type | SeqcAda.index |
|---|---|
| Human | s3:https://seqc-public/genomes/hg38_long_polya/ |
| Mouse | s3:https://seqc-public/genomes/mm38_long_polya/ |
conda activate scing
./submit.sh \
-k ~/keys/cromwell-secrets.json \
-i configs/your-sample.inputs.json \
-l configs/your-sample.labels.json \
-o SeqcAda.options.aws.json