{"action":"created","issue":{"url":"https://api.github.com/repos/gtamazian/chromosomer/issues/11","repository_url":"https://api.github.com/repos/gtamazian/chromosomer","labels_url":"https://api.github.com/repos/gtamazian/chromosomer/issues/11/labels{/name}","comments_url":"https://api.github.com/repos/gtamazian/chromosomer/issues/11/comments","events_url":"https://api.github.com/repos/gtamazian/chromosomer/issues/11/events","html_url":"https://github.com/gtamazian/chromosomer/issues/11","id":188727545,"number":11,"title":"alignment","user":{"login":"colindaven","id":6094884,"avatar_url":"https://avatars.githubusercontent.com/u/6094884?v=3","gravatar_id":"","url":"https://api.github.com/users/colindaven","html_url":"https://github.com/colindaven","followers_url":"https://api.github.com/users/colindaven/followers","following_url":"https://api.github.com/users/colindaven/following{/other_user}","gists_url":"https://api.github.com/users/colindaven/gists{/gist_id}","starred_url":"https://api.github.com/users/colindaven/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/colindaven/subscriptions","organizations_url":"https://api.github.com/users/colindaven/orgs","repos_url":"https://api.github.com/users/colindaven/repos","events_url":"https://api.github.com/users/colindaven/events{/privacy}","received_events_url":"https://api.github.com/users/colindaven/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2016-11-11T10:15:02Z","updated_at":"2016-11-30T14:05:19Z","closed_at":null,"body":"Hi,\r\n\r\nI too  have a question about the docs. Do you recommend a particular aligner ? \r\n\r\nWhich settings should be used ?\r\n\r\nIf a simple example could just be displayed in the Readme this would be very convenient, I don't think an entire website is really necessary for my purposes.\r\n\r\nThanks,\r\nColin"},"comment":{"url":"https://api.github.com/repos/gtamazian/chromosomer/issues/comments/263881085","html_url":"https://github.com/gtamazian/chromosomer/issues/11#issuecomment-263881085","issue_url":"https://api.github.com/repos/gtamazian/chromosomer/issues/11","id":263881085,"user":{"login":"gtamazian","id":5573569,"avatar_url":"https://avatars.githubusercontent.com/u/5573569?v=3","gravatar_id":"","url":"https://api.github.com/users/gtamazian","html_url":"https://github.com/gtamazian","followers_url":"https://api.github.com/users/gtamazian/followers","following_url":"https://api.github.com/users/gtamazian/following{/other_user}","gists_url":"https://api.github.com/users/gtamazian/gists{/gist_id}","starred_url":"https://api.github.com/users/gtamazian/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gtamazian/subscriptions","organizations_url":"https://api.github.com/users/gtamazian/orgs","repos_url":"https://api.github.com/users/gtamazian/repos","events_url":"https://api.github.com/users/gtamazian/events{/privacy}","received_events_url":"https://api.github.com/users/gtamazian/received_events","type":"User","site_admin":false},"created_at":"2016-11-30T14:05:19Z","updated_at":"2016-11-30T14:05:19Z","body":"Hi Colin,\r\n\r\nSorry for my late reply. I would advise to start with the **blastn** aligner from NCBI BLAST+ package. You may try the following **blastn** options for aligning genome fragments to reference chromosomes:\r\n```\r\n-evalue 0.00001 -perc_identity 80 -max_hsps 2\r\n```\r\n\r\nRegards,\r\nGaik"}}
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