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- SRA search page http://www.ncbi.nlm.nih.gov/sra.
- Type in SRX112044 ? Search
- On experiment summary page click SRR390925
- takes you to the Run browser where you can see example reads
- Under "Download", "Run" click "ftp" under .sra
- save the file locally
- Open a Terminal window, change into the directory where the file was stored
- Copy from local machine to TACC
Code Block scp SRR390925.sra username@lonestar.tacc.utexas.edu:~/
- the colon ( : ) after the hostname indicates this is a remote destination
- the ~/ indicates your home directory
- Login to Lonestar:
Code Block ssh username@lonestar.tacc.utexas.edu:~/
- check that the file is in your home directory
Code Block login2$ ls SRR390925.sra
- check that the file is in your home directory
- Find the SRA toolkit module
Code Block login2$ module spider sratoolkit ---------------------------------------------------------------------------- sratoolkit: sratoolkit/2.1.9 ---------------------------------------------------------------------------- Description: The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. This module can be loaded directly: module load sratoolkit/2.1.9 Help: The sratoolkit module file defines the following environment variables: TACC_SRATOOLKIT_DIR for the location of the sratoolkit distribution. Version 2.1.9
- Load the module
Code Block login2$ module load sratoolkit
- Using the environment variable described in spider, invoke fastq-dump with no arguments to get basic usage
Code Block login2$ $TACC_SRATOOLKIT_DIR/fastq-dump Usage: /opt/apps/sratoolkit/2.1.9//fastq-dump [options] [ -A ] <accession> /opt/apps/sratoolkit/2.1.9//fastq-dump [options] <path [path...]> Use option --help for more information /opt/apps/sratoolkit/2.1.9//fastq-dump : 2.1.9
- Extract to fastq
Code Block login2$ $TACC_SRATOOLKIT_DIR/fastq-dump SRR390925.sra Written 1981132 spots for SRR390925.sra Written 1981132 spots total
- Look at some data
Code Block login2$ ls
SRR390925.fastq SRR390925.sra
login2$ head SRR390925.fastq
@SRR390925.1 ROCKFORD:1:1:0:1260 length=36
NCAACAAGTTTCTTTGGTTATTAACTACGACTTACC
\+SRR390925.1 ROCKFORD:1:1:0:1260 length=36
\#CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
@SRR390925.2 ROCKFORD:1:1:0:293 length=36
NAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
\+SRR390925.2 ROCKFORD:1:1:0:293 length=36
\####################################
@SRR390925.3 ROCKFORD:1:1:0:330 length=36
codeNAAAAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAA
UCSC Genome Browser Exercises
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