Skip to content

History creation instructions for Workflow tutorial

Use this set of instructions to create the base history for the "Extract Workflow" section of the workflows tutorial.

Step 1: Import the raw datafiles

  • Create a new blank history by clicking on the history menu , then Create New
  • Use the upload data tool to upload the data files from a remote repository..
    • Click Get Data -> Upload File
    • Click Paste/Fetch data
    • In the box paste the following two url's (one per line): https://swift.rc.nectar.org.au:8888/v1/AUTH_377/public/COMP90014/Assignment1/bacterial_std_err_1.fastq.gz and https://swift.rc.nectar.org.au:8888/v1/AUTH_377/public/COMP90014/Assignment1/bacterial_std_err_2.fastq.gz
    • Change the Type to fastqsanger
    • Click the Paste/Fetch data button again.
    • Paste https://swift.rc.nectar.org.au:8888/v1/AUTH_377/public/COMP90014/Assignment1/Ecoli-O157_H7-Sakai-chr.fna
    • Change the Type on this file to fasta
    • Click the Start button.
    • Click the Close button.

After the import is complete, you should have 3 files in your history. 2 fastq files and a fasta file.

Step 2: Run BWA

Now we will run BWA on these files to map the reads to the reference.

  • In the tools menu, click NGS: Mapping -> Map with BWA
  • Set the following in the tool interface:
    • "Will you select a reference genome from your history or use a built-in index?": Use a genome from history and build index
    • "Use the following dataset as the reference sequence": https://swift.rc.nectar.org.au:8888/v1/AUTH_377/public/COMP90014/Assignment1/Ecoli-O157_H7-Sakai-chr.fna
    • "Select first set of reads": https://swift.rc.nectar.org.au:8888/v1/AUTH_377/public/COMP90014/Assignment1/bacterial_std_err_1.fastq
    • "Select second set of reads": https://swift.rc.nectar.org.au:8888/v1/AUTH_377/public/COMP90014/Assignment1/bacterial_std_err_2.fastq
  • Click Execute

This will run BWA and result in an output compressed BAM file containing the mapping information for all of the reads versus the reference.

Step 3: Run Freebayes

Now we will run Freebayes to call variants in out reads compared with the reference.

  • In the tools menu, click NGS: Variant Analysis -> Freebayes
  • Set the following in the tool interface:
    • "Choose the source for the reference genome": History
    • "BAM file": Map with BWA on data 2, data 1, and data 3 (mapped reads in BAM format)
    • "Use the following dataset as the reference sequence": https://swift.rc.nectar.org.au:8888/v1/AUTH_377/public/COMP90014/Assignment1/Ecoli-O157_H7-Sakai-chr.fna
  • Click Execute

This will run Freebayes on your BAM file and will result in a variant calling format file (vcf).

Step 4: Filter the VCF file.

Now we will filter the vcf file to something sensible.

  • In the tools menu, click Filter and Sort -> Filter
  • Set the following in the tool interface:
    • "Filter": FreeBayes on data 3 and data 4 (variants)
    • "With following condition": c6 > 500
    • "Number of header lines to skip": 56
  • Click Execute

This will filter out VCF file.

You should now have the requisite history to enable you to complete the workflow extraction section of the workflows tutorial.

Return to it here