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
Community Data > iplantcollaborative > example_data > ncbi_sra_toolkit_fastq_dump
Use SRR4101052.sra as a test input file.
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 section below.
Expect a FASTQ file named after the accession as output.
ChIPseq Using the iPlant Discovery Environment