So I have metagenome bam files which contain reads for both human and bacteria. I would like to remove all the human reads so I can focus on the bacterial reads. Has anyone been able to remove human reads from their RNA-seq data using samtools or any other software?
Align your reads to the human genome first, then extract all the unmapped reads to work with further. The unmapped reads will have all your bacteria (as well as other non-human things). Extracting unmapped paired end from an alignment - C: Extracting unmapped paired end from an alignment