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titleIf you need a little help click the triangle...
Code Block
mkdir fastq
mkdir reference
cp $BI/gva_course/mixed_population/*.fastq fastq

cp $BI/gva_course/mixed_population/REL606.6.gbk reference

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titleIf you need a little help click the triangle...

Be sure to make a new folder named Logs or these commands will fail.

Code Block
breseq -j 6 -p -o breseq_output/with_stats -r reference/REL606.6.gbk fastq/REL964_TACAGCA_L003_R1_002.fastq fastq/REL964_TACAGCA_L003_R2_002.fastq >& Logs/with_stats.log.txt
breseq -j 6 -p -b 0 --polymorphism-score-cutoff 0 --polymorphism-bias-cutoff 0 --polymorphism-minimum-coverage-each-strand 0 -o breseq_output/without_stats -r reference/REL606.6.gbk fastq/REL964_TACAGCA_L003_R1_002.fastq fastq/REL964_TACAGCA_L003_R2_002.fastq >& Logs/without_stats.log.txt

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