Page Comparison

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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
  language bash
  scp SRR390925.sra username@lonestarusername@stampede.tacc.utexas.edu:~/

  • the colon ( : ) after the hostname indicates this is a remote destination
  • the ~/ indicates your home directory

• Login to Lonestar stampede:

  Code Block
  language bash
  ssh username@lonestarusername@stampede.tacc.utexas.edu:~/

  • check that the file is in your home directory

    login2$

    Code Block
    language bash
    stamp:~ ls SRR390925.sra

• Find the SRA toolkit module

  login2$

  Code Block
  language bash
  stamp:~ 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

  login2$

  Code Block
  language bash
  stamp:~ module load sratoolkit

• Invoke fastq-dump with no arguments to get basic usage

  login2$

  Code Block
  language bash
  stamp:~ 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

  login2$

  Code Block
  language bash
  stamp:~ $TACC_SRATOOLKIT_DIR/fastq-dump SRR390925.sra Written 1981132 spots for SRR390925.sra Written 1981132 spots total

• Look at some data

  login2$

  Code Block
  language bash
  stamp:~ ls SRR390925.fastq SRR390925.sra login2$ stamp:~ 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 NAAAAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAA

• Count lines and number of reads (fastq has 4 lines/read)

  login2$

  Code Block
  language bash
  stamp:~ wc -l SRR390925.fastq 7924528 SRR390925.fastq login2$ echo $((7924528 / 4)) 1981132

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