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Map reads to random stuff using bowtie2

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Name		Name	Last commit message	Last commit date
Latest commit History 6 Commits
README.md		README.md
bt2-index.sh		bt2-index.sh
bt2-map.sh		bt2-map.sh
mapto.sh		mapto.sh

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Map reads to reference sequence

Set up conda environments

bowtie2

mamba create -n bowtie2 -c bioconda bowtie2 samtools

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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