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mkdir fastq
mkdir reference
cp $BI/gva_course/mixed_population/*.fastq fastq
cp $BI/gva_course/mixed_population/REL606.6.gbk reference

module load bowtie/2.1.0

The above must be run for breseq to work

By default breseq preforms several statistical tests to rule out false positives. To make use of these tests, simply add a -p flag to any breseq command. To highlight what breseq is normally doing by default we will run the same fastq files with and without several of the statistical tests. Specifically, base quality scores, polymorphism scores, polymorphism bias, and minimum strand coverage will be ignored. All 4 of these arguments can be found in the breseq -h output and their values should be set to 0. While running breseq in polymorphism mode is a fairly simple,  due to the complexity of the command with turning off all the additional options, it is recommended that you copy paste these commands into a commands file or an idev session.

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