SRA-Import-0.1.0

Owned by Roger Barthelson
Last updated: Apr 04, 2017 by kkennedy
1 min read

This app takes an SRR number (SRA database run number) as input, and downloads an SRA file, then converts the SRA file to a fastq file.

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

Description and Quick Start

Imports a SRA file and converts it to fastq format. Takes a SRA run number as input. 

Test Data

/iplant/home/shared/iplantcollaborative/example_data/SRAImport 

No input file is required. An SRR number, that is the Run number associated with an SRA record at NCBI, is required. Example SRR486102

NO Parameters Used with this App

Output File(s)

This app downloads the SRA file, and then runs fastq-dump to extract the fastq file. Both files are provided.

References