how to be aware of multi mapping??

Question

[zizigolu]

friends,

how i can be aware of the rate of multi mapping and its influence on the results from the bowtie2 output?

thank you

[h.mon]

samtools flagstat

[zizigolu]

thanks a lot

[Ashutosh Pandey]

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.

[zizigolu]

thank you Ashutosh