NCBI SRA Import 1.2
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.
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
- To use NCBI SRA Import 1.2, import your data in .sra format.
- Resources: https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc
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