hisplan / seqc-ada

SEQC Ada (AutomateD Analysis)

SEQC Ada

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.

Workflow

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 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.json
• configs/template.labels.json

Assay

Type	SeqcAda.assay
10x v2 Kit	ten_x_v2
10x v3 Kit	ten_x_v3
10x NextGEM	ten_x_v3

Genome Index

Use one of the URLs below for the reference genome:

Type	SeqcAda.index
Human	s3://seqc-public/genomes/hg38_long_polya/
Mouse	s3://seqc-public/genomes/mm38_long_polya/

Submit Your Job

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