{"action":"created","issue":{"url":"https://api.github.com/repos/arq5x/poretools/issues/64","labels_url":"https://api.github.com/repos/arq5x/poretools/issues/64/labels{/name}","comments_url":"https://api.github.com/repos/arq5x/poretools/issues/64/comments","events_url":"https://api.github.com/repos/arq5x/poretools/issues/64/events","html_url":"https://github.com/arq5x/poretools/issues/64","id":114583107,"number":64,"title":"Standardizing read names","user":{"login":"mw55309","id":1777488,"avatar_url":"https://avatars.githubusercontent.com/u/1777488?v=3","gravatar_id":"","url":"https://api.github.com/users/mw55309","html_url":"https://github.com/mw55309","followers_url":"https://api.github.com/users/mw55309/followers","following_url":"https://api.github.com/users/mw55309/following{/other_user}","gists_url":"https://api.github.com/users/mw55309/gists{/gist_id}","starred_url":"https://api.github.com/users/mw55309/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mw55309/subscriptions","organizations_url":"https://api.github.com/users/mw55309/orgs","repos_url":"https://api.github.com/users/mw55309/repos","events_url":"https://api.github.com/users/mw55309/events{/privacy}","received_events_url":"https://api.github.com/users/mw55309/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":4,"created_at":"2015-11-02T12:17:42Z","updated_at":"2015-11-02T12:58:18Z","closed_at":null,"body":"Again, I think poretools began the trend of adding \"_twodirections\" to the read ID (for 2D reads).  I'm not sure I like it.\r\n\r\nThere are no standards, but I guess what comes from the Illumina world is that relationships between reads are embedded in the filenames containing those reads, and the order within those files (_R1.fastq and _R2.fastq).  It's not perfect, but it avoids altering the read IDs (and we should always avoid altering primary data), and means we don't need to do string manipulation on read IDs before comparing them (or do partial string matching).\r\n\r\nIf we absolutely, 100% think we need to change the read identifiers, can I suggest:\r\n\r\n.2d\r\n.t\r\n.c\r\n\r\nwhich is a lot simpler?  (this is quite similar to the /1 and /2 from old Illumina/Solexa identifiers, which were done away with, presumably for a reason)\r\n\r\nCheers\r\nMick\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/arq5x/poretools/issues/comments/153009761","html_url":"https://github.com/arq5x/poretools/issues/64#issuecomment-153009761","issue_url":"https://api.github.com/repos/arq5x/poretools/issues/64","id":153009761,"user":{"login":"mw55309","id":1777488,"avatar_url":"https://avatars.githubusercontent.com/u/1777488?v=3","gravatar_id":"","url":"https://api.github.com/users/mw55309","html_url":"https://github.com/mw55309","followers_url":"https://api.github.com/users/mw55309/followers","following_url":"https://api.github.com/users/mw55309/following{/other_user}","gists_url":"https://api.github.com/users/mw55309/gists{/gist_id}","starred_url":"https://api.github.com/users/mw55309/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mw55309/subscriptions","organizations_url":"https://api.github.com/users/mw55309/orgs","repos_url":"https://api.github.com/users/mw55309/repos","events_url":"https://api.github.com/users/mw55309/events{/privacy}","received_events_url":"https://api.github.com/users/mw55309/received_events","type":"User","site_admin":false},"created_at":"2015-11-02T12:58:18Z","updated_at":"2015-11-02T12:58:18Z","body":"Hmm, OK.  This solves one problem but creates another, in that I can only assume the template and complement sequences do not have \"_Basecall_2D_000_2d\".  In other words information is embedded in the read ID that differs between template, complement and 2D.\r\n\r\nI wonder if we can influence ONT to adopt a tag=value system?"}}