Bamcoverage unique mapping reads

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4.4 years ago

liang795 ▴ 10

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!

RNA-Seq bamcoverage multiplemapping • 1.6k views

ADD COMMENT • link updated 3.5 years ago by tim.ivanov.92 ▴ 40 • written 4.4 years ago by liang795 ▴ 10

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You can try the bamCoverage options --minMappingQuality, --samFlagInclude or --samFlagExclude to 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.

ADD REPLY • link 4.4 years ago by h.mon 35k

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How can i specify the SAM file flag NH=1 into option --samFlagInclude? what is the SAM flag code for this?

ADD REPLY • link 3.5 years ago by tim.ivanov.92 ▴ 40

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