fastq-dump is a part of the NCBI SRA Toolkit. It converts archive files in the SRA format into FASTQ format suitable for downstream analysis.
- To use fastq-dump, upload your data in SRA format and then specify the SRA accession name represented by that file. Most of the time, the filename (such as SRR012345.lite.sra) gives this information.
- Resources: documentation
All files are located in the Community Data directory of the iPlant Discovery Environment at the following path:
Community Data > iplantcollaborative > example_data > ncbi_sra_toolkit_fastq_dump
- Use SRR070570.lite.sra as a test input file.
Parameters Used in App
When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.
- Expect a FASTQ file named after the accession as output.