How to extract unique reads from SAM file

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Hi.
How can I extract uniquely and concordantly paired-end mapped reads (aligned concordantly exactly 1 time) from HISAT2?
Thanks

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I think you want samtools view:
https://usegalaxy.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8
e.g.:

image
image.png392×799 41.9 KB

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