How to filter unique reads from sam file?
How to extract unique mapped reads from sam alignment file of pair end reads
The mapping was done using bowtie2.
There are different posts for the same topic suggesting to use the 11 , 12 columns AS and XS
Others say Unique alignments in bowtie2 have MAPQ>=2 and which option shall I use for bowtie2 to get an option like -m from bowtie?
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