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You can use samtools view -q 1 to only output uniquely mapped reads (and omit both unmapped and ambiguous ones). Ambiguous reads that can be mapped to different locations with the same score have mapping quality 0 in BWA.
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ID'ing Uniquely Mapped Regions in BWA
I have another BWA inquiry. How can one id the uniquely mapped reads from a sam/bam generated by BWA? Thanks for any thoughts.Tags: None
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The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...-
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