{"action":"created","issue":{"url":"https://api.github.com/repos/marbl/canu/issues/573","repository_url":"https://api.github.com/repos/marbl/canu","labels_url":"https://api.github.com/repos/marbl/canu/issues/573/labels{/name}","comments_url":"https://api.github.com/repos/marbl/canu/issues/573/comments","events_url":"https://api.github.com/repos/marbl/canu/issues/573/events","html_url":"https://github.com/marbl/canu/issues/573","id":246779034,"number":573,"title":"Use previously correct sequences for new trimming and assembly processes","user":{"login":"uceleste","id":30322535,"avatar_url":"https://avatars1.githubusercontent.com/u/30322535?v=4","gravatar_id":"","url":"https://api.github.com/users/uceleste","html_url":"https://github.com/uceleste","followers_url":"https://api.github.com/users/uceleste/followers","following_url":"https://api.github.com/users/uceleste/following{/other_user}","gists_url":"https://api.github.com/users/uceleste/gists{/gist_id}","starred_url":"https://api.github.com/users/uceleste/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/uceleste/subscriptions","organizations_url":"https://api.github.com/users/uceleste/orgs","repos_url":"https://api.github.com/users/uceleste/repos","events_url":"https://api.github.com/users/uceleste/events{/privacy}","received_events_url":"https://api.github.com/users/uceleste/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2017-07-31T14:36:52Z","updated_at":"2017-07-31T19:19:16Z","closed_at":"2017-07-31T19:19:16Z","body":"Dear All,\r\n\r\nI did a first assembly test with Canu doing all of the three steps and using a command line like this:\r\n\r\n```\r\n$ canu -p Name -d Name genomeSize=Size corOutCoverage=200 -pacbio-raw Dataset.fa\r\n```\r\n\r\nNow I would like to make a further test by entering the specific parameters for heterozygosity and using the same corrected dataset obtained from the first assembly. Can I only perform the trimming and assembly processes using the corrected dataset with a command like this?\r\n\r\n```\r\n$ canu -trim-assembly -p Name -d Name genomeSize=Size corOutCoverage=200 ovlErrorRate=0.15 obtErrorRate=0.15 -pacbio-corrected Name.correctedReads.fasta.gz\r\n```\r\n\r\nIs the corOutCoverage=200 parameter specific to the correction phase only? Can it be deleted from this command line?\r\n\r\nThank you ever so much!"},"comment":{"url":"https://api.github.com/repos/marbl/canu/issues/comments/319169003","html_url":"https://github.com/marbl/canu/issues/573#issuecomment-319169003","issue_url":"https://api.github.com/repos/marbl/canu/issues/573","id":319169003,"user":{"login":"skoren","id":923478,"avatar_url":"https://avatars2.githubusercontent.com/u/923478?v=4","gravatar_id":"","url":"https://api.github.com/users/skoren","html_url":"https://github.com/skoren","followers_url":"https://api.github.com/users/skoren/followers","following_url":"https://api.github.com/users/skoren/following{/other_user}","gists_url":"https://api.github.com/users/skoren/gists{/gist_id}","starred_url":"https://api.github.com/users/skoren/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/skoren/subscriptions","organizations_url":"https://api.github.com/users/skoren/orgs","repos_url":"https://api.github.com/users/skoren/repos","events_url":"https://api.github.com/users/skoren/events{/privacy}","received_events_url":"https://api.github.com/users/skoren/received_events","type":"User","site_admin":false},"created_at":"2017-07-31T19:19:16Z","updated_at":"2017-07-31T19:19:16Z","body":"Yes, ```corOutCoverage``` is specific to assembly and can be deleted. You also don't need to specify the ```-trim-assembly``` option, providing pacbio-corrected reads automatically selects that option.\r\n\r\nThe error rate you are using is relatively high (15%) so this will likely be much slower than the default assembly which uses 5% (or 1/3) the error rate."}}
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