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