This pipeline is designed to process RNA-Seq data generated by total RNA-Seq strategy. One advantage of total RNA-Seq strategy is it can capture and sequence both linear and circular mRNA isoforms at a single run. circRNA is not considered in most existing gene expression quantification tools and pipelines which focused on polyA enriched RNA-Seq data. To solve this problem, we designed this total RNA-Seq analysis pipeline. It identifies circRNAs from total RNA-Seq first. Then, RNA-Seq reads will be distributed to linear and circular mRNA isoforms to quantify their expression.

Quick Start

1. Install Nextflow (>=21.04.1)
2. Install docker for pipeline reproducibility
3. Prepare a case ID file (see documentation for file format)
4. Run a test with 2 samples on local server.

nextflow run bzhanglab/nf-rnaseq -r main -profile docker \
   --case_id /path/to/my_case_id.txt \
   --start 1 --end 2 --run_version rnaseq-2021-01-01

5. Run with AWS batch on AWS cloud, see here for proper configuration of your AWS environment.

nextflow run bzhanglab/nf-rnaseq -r main -profile awsbatch \
   --start 1 --end 2 \
   --case_id /path/to/my_case_id.txt \
   -bucket-dir s3://zhanglab-nextflow-workdir/workdir/2021-01-01 \
   --outdir /path/to/rnaseq-results \
   --run_version rnaseq-2021-01-01