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Find and download RNAseq data from run SRR390925, of experiment SRX112044, publication SRP009873. Copy the file to your Scratch area home directory on Stampede2 Lonestar at TACC then extract the data in FASTQ fastq format.

A solution

• SRA search page http://www.ncbi.nlm.nih.gov/sra.
• Type in SRX112044 then ? Search
• On experiment summary page click SRR390925
  • takes you to the Run browser where you can see example reads
• Under "Download" tab, select Reads
  
  • This tells you that you need the SRA Toolkit to fetch the Run data

  Login to stampede2:

  Code Blockssh username@stampede2, "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 Scratch areahome directory

    Code Block
    language bash title Once on stampede2 (prompt: stamp2$)
    cds login2$ ls SRR390925.sra

    if not, copy it from our course area:

    Once on stampede2 (prompt: stamp2$)

    Code Block
    language	bash
    title

• Find the SRA toolkit module

  Code Block

  module load biocontainerslogin2$ module spider sratoolkit ------------------------------------------------------------------------------------------------------ sratoolkit: sratoolkit/2.81.2 -------------------------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/2.81.29 Help: The sratoolkit module file defines the following environment variables: - TACC_SRATOOLKSRATOOLKIT_DIR - TACC_SRATOOLK_EXAMPLE - example files To improve download speed,for the prefetch command has been aliased to always use aspera. We also suggest running $ scratch_cache to change your cache directory to use the scratch filesystem. Documentation can be found online at https://github.com/ncbi/sra-tools/wikilocation of the sratoolkit distribution. Version 2.81.29

• Load the module

  Code Block
  login2$ module load sratoolkit

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

  Code Block
  login2$ fastq-dump Usage: /opt/apps/sratoolkit/2.1.9//fastq-dump [options] [ <path> [<path>...]-A ] <accession> /opt/apps/sratoolkit/2.1.9//fastq-dump [options] <accession> <path [path...]> Use option --help for more information /opt/apps/sratoolkit/2.1.9//fastq-dump : 2.81.29

• Extract to FASTQ fastq

  Code Block
  login2$ $TACC_SRATOOLKIT_DIR/fastq-dump SRR390925.sra # Output should look like this: 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 NAAAAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAA

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

  Code Block
  login2$ wc -l SRR390925.fastq 7924528 SRR390925.fastq login2$ echo $((7924528 / 4)) 1981132

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