How to remove reads mapped to both plasmid and chromosome from the .sam file?

How to remove reads mapped to both plasmid and chromosome from the .sam file?

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I have a .sam file with reads mapped to a plasmid and a bacterial chromosome. I used bowtie to map reads and I allowed multi-mapping.

How can I exclude reads which were aligned to both plasmid and chromosome from the .sam file? I want to do this in order to avoid biases caused by different plasmid copy numbers


SAM-file


NGS


small-RNA

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