{"action":"closed","issue":{"url":"https://api.github.com/repos/marcus1487/nanoraw/issues/47","repository_url":"https://api.github.com/repos/marcus1487/nanoraw","labels_url":"https://api.github.com/repos/marcus1487/nanoraw/issues/47/labels{/name}","comments_url":"https://api.github.com/repos/marcus1487/nanoraw/issues/47/comments","events_url":"https://api.github.com/repos/marcus1487/nanoraw/issues/47/events","html_url":"https://github.com/marcus1487/nanoraw/issues/47","id":263314796,"number":47,"title":"Issue with extracting out the sequence with genome_resquiggle with direct RNA sequencing","user":{"login":"awjga","id":30524842,"avatar_url":"https://avatars1.githubusercontent.com/u/30524842?v=4","gravatar_id":"","url":"https://api.github.com/users/awjga","html_url":"https://github.com/awjga","followers_url":"https://api.github.com/users/awjga/followers","following_url":"https://api.github.com/users/awjga/following{/other_user}","gists_url":"https://api.github.com/users/awjga/gists{/gist_id}","starred_url":"https://api.github.com/users/awjga/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/awjga/subscriptions","organizations_url":"https://api.github.com/users/awjga/orgs","repos_url":"https://api.github.com/users/awjga/repos","events_url":"https://api.github.com/users/awjga/events{/privacy}","received_events_url":"https://api.github.com/users/awjga/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2017-10-06T01:44:26Z","updated_at":"2017-10-06T21:19:08Z","closed_at":"2017-10-06T21:19:08Z","author_association":"NONE","body":"Hi,\r\n\r\nI would like to highlight an issue about the extracting of the sequences from the basecalled fast5 to be used in mapping for genome_resquiggle.\r\n\r\nFrom my understanding of your code, you are extracting the character middle of \"model_state\", and the value in \"move\" must be greater than 0. \r\nThe extracted character would be combined and will be used for mapping.\r\n\r\nThe extraction of the sequences is based on the assumption the most of the signal would only move by 1 nucleotide?\r\nThis is where the issue is.\r\nAs I am using direct RNA sequencing, ~16% of my signal in 1 read have the move value = 2, and it occurs throughout the read.\r\nThus, the extracted sequence from nanoraw is quite different from the basecalled sequences.\r\nAnd the sequence in nanoraw and from albacore will be flipped and there is U instead of T in the albacore sequences, as it is direct RNA sequencing.    \r\nThere is 878 1 and 201 2 in my read and the sequenced length is 1284, and the extracted sequence length from nanoraw  is 1079.\r\n\r\nI have tested this with the control RNA, and it is about 1.2kb long.\r\n\r\n "}}
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