{"issue":{"pull_request":{"diff_url":null,"html_url":null,"patch_url":null},"state":"open","user":{"avatar_url":"https://secure.gravatar.com/avatar/840a3abaf67e9fef8c58225d2e20608a?d=https://a248.e.akamai.net/assets.github.com%2Fimages%2Fgravatars%2Fgravatar-140.png","gravatar_id":"840a3abaf67e9fef8c58225d2e20608a","url":"https://api.github.com/users/brainstorm","login":"brainstorm","id":175587},"milestone":null,"assignee":{"avatar_url":"https://secure.gravatar.com/avatar/8096c7d6bc0d0ee0e67538d947869b3a?d=https://a248.e.akamai.net/assets.github.com%2Fimages%2Fgravatars%2Fgravatar-140.png","gravatar_id":"8096c7d6bc0d0ee0e67538d947869b3a","url":"https://api.github.com/users/vals","login":"vals","id":668803},"labels":[{"name":"asap","color":"02d7e1","url":"https://api.github.com/repos/brainstorm/bcbb/labels/asap"},{"name":"feature","color":"3809f2","url":"https://api.github.com/repos/brainstorm/bcbb/labels/feature"}],"updated_at":"2011-11-07T16:58:04Z","closed_at":null,"comments":13,"url":"https://api.github.com/repos/brainstorm/bcbb/issues/20","body":"Instead of blindly trusting the samplesheet/manually specified barcodes, Clustering them, in order to find contamination or other problems.\r\n\r\nIn other words, we should be able to detect which barcodes are there just by processing the fastq files (since we know that the barcodes are attached at the 3' end by default).\r\n\r\n\r\nSuggested by Ellen, Max and others.","html_url":"https://github.com/brainstorm/bcbb/issues/20","title":"Demultiplex based on barcodes found in reads","number":20,"id":1074028,"created_at":"2011-06-17T15:02:31Z"},"action":"created","comment":{"user":{"avatar_url":"https://secure.gravatar.com/avatar/bf36ba627303241ad267f96b76f2b095?d=https://a248.e.akamai.net/assets.github.com%2Fimages%2Fgravatars%2Fgravatar-140.png","gravatar_id":"bf36ba627303241ad267f96b76f2b095","url":"https://api.github.com/users/hussius","login":"hussius","id":373445},"updated_at":"2011-11-07T16:58:04Z","url":"https://api.github.com/repos/brainstorm/bcbb/issues/comments/2656061","body":"Nice! Just one detail: make sure that you look at the last six but one characters in the sequence row in the FASTQ file. The last base is always supposed to be an A and it's only there because it's needed to estimate the quality score of the last index base, or something like that. The total length of the sequence line is typically 108 (plus a newline character, so 109 if one wants to be picky): 101 proper sequence + 6 index bases + 1 \"A\". ","id":2656061,"created_at":"2011-11-07T16:58:04Z"}}