The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

The box below searches only this space.
To search the entire iPlant wiki, enter your query in the box at the upper right.

 

 

 

 

 

Skip to end of metadata
Go to start of metadata

NCBI SRA Import 1.2

Import NCBI SRA files into the CyVerse environment using the fasp protocol. This application uses the new aspera-connect-3.1.1 program code.

Icon

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

Matthew Vaughn

Quick Start

Test Data

Use these files from the ftp directory of NCBI as test input:

ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR636/SRR636574/SRR636574.sra 

ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR636/SRR636575/SRR636575.sra 

Input File(s)

This app only requires the .sra files from the NCBI ftp. No other input files are required. 

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.

  • Default parameters only, no further configuration needed.

Output File(s)

For the test case, expect  SRR636574.sra and SRR636575.sra 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=toolkit_doc

  • No labels