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.

Quick Start

• 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

Test Data

All files are located in the Community Data directory of the CyVerse Discovery Environment at the following path:

Community Data > iplantcollaborative > example_data > ncbi_sra_toolkit_fastq_dump

Input File(s)

Use SRR4101052.sra  as a test input file.

Or

Use SRR4101052

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 section below.

Output File(s)

Expect a FASTQ file named after the accession as output.

Related Tutorials

ChIPseq Using the iPlant Discovery Environment

Tool Source for App

https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software

https://edwards.sdsu.edu/research/fastq-dump/