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NGS Practical

NGS Practical . Exome Analysis. Prepare data and tools. Download tools bundle ( exome_bin.zip ) from: ftp:// ftp.sanbi.ac.za / junaid / move it to your home directory and uncompress it copy the datafile (from yesterday) into the exome_bin directory that gets created

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NGS Practical

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  1. NGS Practical Exome Analysis

  2. Prepare data and tools • Download tools bundle (exome_bin.zip) from: ftp://ftp.sanbi.ac.za/junaid/ • move it to your home directory and uncompress it • copy the datafile (from yesterday) into the exome_bin directory that gets created • Go into the directory and uncompress anything that’s compressed

  3. ‘Mini test’ • Make a very small file for testing of 500 sequences: • head -2000 DATAFILE > SMALLDATAFILE • Make a copy of the exome_pipeline.sh script and change first instance of test.fastq to whatever you named your ‘SMALLDATAFILE’ • Make the script copy executable and run it: • ./exome_pipeline_copy.sh

  4. Run the main script • If the script runs through, • Run the main script • ./exome_pipeline.sh • I will put specific questions on the website for the assignment

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