SRA Data Pipeline
The SRA pipeline accepts one or more NCBI SRA run accession IDs (SRR format), downloads the corresponding FASTQ files from NCBI, and runs the same FASTQ pipeline analysis.
Web app slug: sra-data-pipeline
When to use
Section titled “When to use”Use this pipeline when you have public SRA accession IDs and do not need to upload raw files manually. Ideal for reproducing published cohort analyses or processing publicly available datasets.
Submitting a job
Section titled “Submitting a job”Navigate to Dashboard → SRA Data Pipeline → Create New Job.
Required inputs
Section titled “Required inputs”| Field | Description |
|---|---|
| Patient Label | Label for the donor |
| SRR IDs | One or more SRA run accession IDs (comma-separated or one per line), e.g., SRR12345678, SRR12345679 |
| Preset Strategy | The preset strategy for the FASTQ pipeline |
| Chain Type | The type of immune receptor chain (e.g., TRA, TRB, IGH) |
| AIRR Mode | The mode for AIRR formatting |
| Download method | ascp or aria2c method |
Output files
Section titled “Output files”Same as FASTQ Pipeline outputs, with one result set per SRR ID plus a merged summary.