how i can be aware of the rate of multi mapping and its influence on the results from the bowtie2 output?
thanks a lot
Every aligned read has a NH:i: tag associated with it in the SAM format. NH:i:1 means one hit or unique alignment. NH:i:2 means the read can be aligned at multiple places (here two). Most often such reads are not used towards variant calling or RNA-seq count data generation. Shorter reads especially that represent less complex part of the genome or CNV regions usually show multi-mapping.
thank you Ashutosh
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