I want to filter out human 'contaminants' from my metagenomic sample. I mapped my reads to a human genome and I am filtering them with samtools. So far, I only filter out reads that had mapping flag, but should I also add a flag for removing supplementary reads while filtering? I can't wrap my head around the idea of supplementary reads and what they actually mean in terms of filtering.
Question: Filtering human reads in metagenomics: should supplementary reads be removed?
14 months ago by
ciemanek • 140
ciemanek • 140 wrote:
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