{"action":"opened","issue":{"url":"https://api.github.com/repos/BenLangmead/bowtie2/issues/140","repository_url":"https://api.github.com/repos/BenLangmead/bowtie2","labels_url":"https://api.github.com/repos/BenLangmead/bowtie2/issues/140/labels{/name}","comments_url":"https://api.github.com/repos/BenLangmead/bowtie2/issues/140/comments","events_url":"https://api.github.com/repos/BenLangmead/bowtie2/issues/140/events","html_url":"https://github.com/BenLangmead/bowtie2/issues/140","id":257839354,"number":140,"title":"Only one of two paired reads marked \"read mapped in proper pair\" (flag 2) in FLAG field ","user":{"login":"rkageyama","id":8195095,"avatar_url":"https://avatars3.githubusercontent.com/u/8195095?v=4","gravatar_id":"","url":"https://api.github.com/users/rkageyama","html_url":"https://github.com/rkageyama","followers_url":"https://api.github.com/users/rkageyama/followers","following_url":"https://api.github.com/users/rkageyama/following{/other_user}","gists_url":"https://api.github.com/users/rkageyama/gists{/gist_id}","starred_url":"https://api.github.com/users/rkageyama/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rkageyama/subscriptions","organizations_url":"https://api.github.com/users/rkageyama/orgs","repos_url":"https://api.github.com/users/rkageyama/repos","events_url":"https://api.github.com/users/rkageyama/events{/privacy}","received_events_url":"https://api.github.com/users/rkageyama/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2017-09-14T20:02:26Z","updated_at":"2017-09-14T20:02:26Z","closed_at":null,"author_association":"NONE","body":"I have been running bowtie2 on paired end sequences and noticed something funny when I tried to filter out reads that weren't properly paired. I seemed to be getting orphan reads left behind after filtering with `samtools view -f 2`. After digging around, I noticed that after the initial alignment, I was getting reads that were flagged `163` and `113`. \r\n\r\n`NS500418:295:HWG3TBGXX:4:11405:20193:10248\t163\tchr1\t1624577\t255`\r\n\r\n`NS500418:295:HWG3TBGXX:4:11405:20193:10248\t113\tchr1\t1677965\t255`\r\n\r\nRunning `samtools fixmate` changes the flags to `163` and `81` , but that still leaves the bit 2 unaffected. \r\n\r\nAs I understand it, it seems like this means that one of the two is \"read mapped in proper pair\" as indicated by flag 2, but the other one isn't, which I don't think should be possible if I understand it correctly. \r\n\r\nHere is the bowtie command I ran:\r\n\r\n`bowtie2 -k1 -N1 -p16 -x hg19 -1 R1.fastq -2 R2.fastq -S file.sam`\r\n\r\nFound in version 2.1.0, but verified I was still getting the same results in 2.3.3"}}
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