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Map reads to reference sequence

Set up conda environments

  1. bowtie2
mamba create -n bowtie2 -c bioconda bowtie2 samtools
  1. bbmap
mamba create -n bbmap -c bioconda bbmap

Run workflow

Paths etc are hardcoded to scripts, look into and customize as necessary.

bash mapto.sh

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Map reads to random stuff using bowtie2

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