{"action":"created","issue":{"url":"https://api.github.com/repos/percolator/percolator/issues/229","repository_url":"https://api.github.com/repos/percolator/percolator","labels_url":"https://api.github.com/repos/percolator/percolator/issues/229/labels{/name}","comments_url":"https://api.github.com/repos/percolator/percolator/issues/229/comments","events_url":"https://api.github.com/repos/percolator/percolator/issues/229/events","html_url":"https://github.com/percolator/percolator/issues/229","id":359770462,"node_id":"MDU6SXNzdWUzNTk3NzA0NjI=","number":229,"title":"Q values for all PSM's","user":{"login":"StevenVerbruggen","id":15814435,"node_id":"MDQ6VXNlcjE1ODE0NDM1","avatar_url":"https://avatars1.githubusercontent.com/u/15814435?v=4","gravatar_id":"","url":"https://api.github.com/users/StevenVerbruggen","html_url":"https://github.com/StevenVerbruggen","followers_url":"https://api.github.com/users/StevenVerbruggen/followers","following_url":"https://api.github.com/users/StevenVerbruggen/following{/other_user}","gists_url":"https://api.github.com/users/StevenVerbruggen/gists{/gist_id}","starred_url":"https://api.github.com/users/StevenVerbruggen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/StevenVerbruggen/subscriptions","organizations_url":"https://api.github.com/users/StevenVerbruggen/orgs","repos_url":"https://api.github.com/users/StevenVerbruggen/repos","events_url":"https://api.github.com/users/StevenVerbruggen/events{/privacy}","received_events_url":"https://api.github.com/users/StevenVerbruggen/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2018-09-13T07:13:58Z","updated_at":"2018-09-13T12:53:27Z","closed_at":null,"author_association":"NONE","body":"Hi,\r\n\r\nFor our analysis, we are interested in the Q values of all PSM hits. We submit a tab input file of 15 possible hits per spectrum. In the output target psms files where the Q values are shown, only the best-scoring PSM per scan is outputted. We tried by setting the test FDR to 1 in order to not filter on the output, but still only the best-scoring PSM is sent to the output file. We searched in the command line arguments for a parameter to adapt this in the output, but did not found that so far.\r\n\r\nIs there a way to get the Q values of all PSMs?"},"comment":{"url":"https://api.github.com/repos/percolator/percolator/issues/comments/420995832","html_url":"https://github.com/percolator/percolator/issues/229#issuecomment-420995832","issue_url":"https://api.github.com/repos/percolator/percolator/issues/229","id":420995832,"node_id":"MDEyOklzc3VlQ29tbWVudDQyMDk5NTgzMg==","user":{"login":"percolator","id":95488,"node_id":"MDQ6VXNlcjk1NDg4","avatar_url":"https://avatars2.githubusercontent.com/u/95488?v=4","gravatar_id":"","url":"https://api.github.com/users/percolator","html_url":"https://github.com/percolator","followers_url":"https://api.github.com/users/percolator/followers","following_url":"https://api.github.com/users/percolator/following{/other_user}","gists_url":"https://api.github.com/users/percolator/gists{/gist_id}","starred_url":"https://api.github.com/users/percolator/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/percolator/subscriptions","organizations_url":"https://api.github.com/users/percolator/orgs","repos_url":"https://api.github.com/users/percolator/repos","events_url":"https://api.github.com/users/percolator/events{/privacy}","received_events_url":"https://api.github.com/users/percolator/received_events","type":"User","site_admin":false},"created_at":"2018-09-13T12:53:27Z","updated_at":"2018-09-13T12:53:27Z","author_association":"OWNER","body":"Oups! You are right, Matthew.\n\nOn Thu, Sep 13, 2018 at 2:44 PM MatthewThe <notifications@github.com> wrote:\n\n> It's actually the -y flag (--post-processing-mix-max) that controls this.\n>\n> —\n> You are receiving this because you commented.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/percolator/percolator/issues/229#issuecomment-420992912>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/AAF1ABrly_26qkN6LkDbUdbeMFfhGa6mks5ualMagaJpZM4WmsqJ>\n> .\n>\n"}}
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