I have sequencing reads from a non-human primate sequencing project, but also have some human contamination. To remove the contaminants I would like to align the reads to both human and non-human reference genomes then select only the reads which primary alignment is to the non-human primate genome. I know that particular regions can be sub-set using samtools view. However the non-human genome has over 3 million scaffolds is there a way to select all reads by genome rather than by scaffold?
Question: Remove contaminants by aligning to two genomes and selecting reads from one genome using samtools view
3.2 years ago by
aylward.megan • 0
aylward.megan • 0 wrote:
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