Bamcoverage unique mapping reads
Hi Guys
Would bamcoverage only calculate read-pairs if any pair maps to unique locations? As I my bam files were generated with multiple mappings, but for visualization I only want unique mapping locations. Does bamcoverage have this option?
Thanks!
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tim.ivanov.92 •
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liang795 •
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You can try the bamCoverage options
--minMappingQuality,--samFlagIncludeor--samFlagExcludeto take into account only unique properly paired reads. How to set these parameters will probably depend on the program and arguments you used for mapping.How can i specify the SAM file flag NH=1 into option --samFlagInclude? what is the SAM flag code for this?