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{"@context":"https://schema.org","@type":"DiscussionForumPosting","headline":"Question: Does two reads with opposite strand with same mapping location regarded as duplicates?","articleBody":"Hi Andrew, \r\n\r\nI have a nanopore sequencing library where one molecule could result in reads on both forward or reverse strands. I would like to know if preseq regard these pairs as \"distinct\" observation, or as \"repeated\" observation? \r\n\r\nThe definition of \"distinct\" observation is not very clearly stated in the documentation. I was trying to find it in the implementation:\r\n\r\nRelated lines: \r\nhttps://github.com/smithlabcode/preseq/blob/c0fc953764029728d0c1e8fb7b33464b041794c5/src/load_data_for_complexity.cpp#L90\r\nRelated class: [GenomicRegion.hpp](https://github.com/smithlabcode/smithlab_cpp/blob/23c6c50c96fff166477bfd90b3e7e3b10557c14b/GenomicRegion.hpp\r\n)\r\n\r\nIt seems like get_start() is getting the smaller coordinate of a bam read? \r\nIf so, does it mean that both reverse and forward-mapped reads would be seen as the same molecule (same 'start') -- This is the desired behavior in my use case.\r\n\r\nI would love to hear from you! \r\n\r\nThe command I used:\r\n```\r\n./preseq lc_extrap -B -o ./yield-estimates.txt \u003cinput-sorted-bam\u003e\r\n```\r\nSoftware version: \r\nv2.0 downloaded [precompiled binary\r\n](http://smithlabresearch.org/software/preseq/)\r\n\r\nBest, \r\nLi-Ting \r\n\r\n","author":{"url":"https://github.com/zztin","@type":"Person","name":"zztin"},"datePublished":"2023-07-05T09:43:00.000Z","interactionStatistic":{"@type":"InteractionCounter","interactionType":"https://schema.org/CommentAction","userInteractionCount":1},"url":"https://github.com/67/preseq/issues/67"}