{"action":"opened","issue":{"url":"https://api.github.com/repos/boutroslab/CRISPRAnalyzeR/issues/15","repository_url":"https://api.github.com/repos/boutroslab/CRISPRAnalyzeR","labels_url":"https://api.github.com/repos/boutroslab/CRISPRAnalyzeR/issues/15/labels{/name}","comments_url":"https://api.github.com/repos/boutroslab/CRISPRAnalyzeR/issues/15/comments","events_url":"https://api.github.com/repos/boutroslab/CRISPRAnalyzeR/issues/15/events","html_url":"https://github.com/boutroslab/CRISPRAnalyzeR/issues/15","id":213668447,"number":15,"title":"Bowtie2 Invalid Sensitivity Options","user":{"login":"DarioS","id":631218,"avatar_url":"https://avatars1.githubusercontent.com/u/631218?v=3","gravatar_id":"","url":"https://api.github.com/users/DarioS","html_url":"https://github.com/DarioS","followers_url":"https://api.github.com/users/DarioS/followers","following_url":"https://api.github.com/users/DarioS/following{/other_user}","gists_url":"https://api.github.com/users/DarioS/gists{/gist_id}","starred_url":"https://api.github.com/users/DarioS/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/DarioS/subscriptions","organizations_url":"https://api.github.com/users/DarioS/orgs","repos_url":"https://api.github.com/users/DarioS/repos","events_url":"https://api.github.com/users/DarioS/events{/privacy}","received_events_url":"https://api.github.com/users/DarioS/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2017-03-13T04:00:22Z","updated_at":"2017-03-13T04:00:22Z","closed_at":null,"body":"The application offers `choices = list(\"very-sensitive-local\", \"local\", \"very-sensitive\"))` for setting the Bowtie 2 sensitivity. However, `\"very-sensitive\"` is only applicable in end-to-end mapping mode whereas the `\"very-sensitive-local\"` is only valid for local alignment mode. According to Ben Langmead BenLangmead/bowtie2#66, the default end-to-end alignment of Bowtie 2 is not suitable if the read (e.g. 21 nucleotides) is longer than the reference sequence (e.g. 20 nucleotides). Bowtie 2 needs to be run with the `--local` option and in the Shiny application, `\"very-sensitive\"` is not a valid option for this kind of alignment so should be removed and replaced. Note that `\"local\"` is a mapping mode, not a sensitivity level, so it's also not a valid value for mapping sensitivity. For reference, valid sensitivity values are:\r\n\r\n```\r\nPreset options in --end-to-end mode\r\n--very-fast         Same as: -D 5 -R 1 -N 0 -L 22 -i S,0,2.50\r\n--fast              Same as: -D 10 -R 2 -N 0 -L 22 -i S,0,2.50\r\n--sensitive         Same as: -D 15 -R 2 -L 22 -i S,1,1.15 (default in --end-to-end mode)\r\n--very-sensitive    Same as: -D 20 -R 3 -N 0 -L 20 -i S,1,0.50\r\n\r\nPreset options in --local mode\r\n--very-fast-local        Same as: -D 5 -R 1 -N 0 -L 25 -i S,1,2.00\r\n--fast-local             Same as: -D 10 -R 2 -N 0 -L 22 -i S,1,1.75\r\n--sensitive-local        Same as: -D 15 -R 2 -N 0 -L 20 -i S,1,0.75 (default in --local mode)\r\n--very-sensitive-local   Same as: -D 20 -R 3 -N 0 -L 20 -i S,1,0.50\r\n```\r\n\r\nThis fix may moderately increase the mapping percentages."}}
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