NCBI SRA Toolkit fastq-dump 2.3.4
NCBI SRA Toolkit fastq-dump 2.3.4
fastq-dump
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.
Although this app is still functional, it does not have the capability of working with the new SRRs or splitting FASTQ files for paired-end reads. If you need that functionality, please use the NCBI-SRA-Fastq-dump-2.8.1 app instead.
App Creator
Roger Barthelson
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 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 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