{"action":"created","issue":{"url":"https://api.github.com/repos/csiro-crop-informatics/biokanga/issues/13","repository_url":"https://api.github.com/repos/csiro-crop-informatics/biokanga","labels_url":"https://api.github.com/repos/csiro-crop-informatics/biokanga/issues/13/labels{/name}","comments_url":"https://api.github.com/repos/csiro-crop-informatics/biokanga/issues/13/comments","events_url":"https://api.github.com/repos/csiro-crop-informatics/biokanga/issues/13/events","html_url":"https://github.com/csiro-crop-informatics/biokanga/issues/13","id":325702124,"number":13,"title":"genGenomeFromAGP help needed","user":{"login":"agroppi","id":5609985,"avatar_url":"https://avatars3.githubusercontent.com/u/5609985?v=4","gravatar_id":"","url":"https://api.github.com/users/agroppi","html_url":"https://github.com/agroppi","followers_url":"https://api.github.com/users/agroppi/followers","following_url":"https://api.github.com/users/agroppi/following{/other_user}","gists_url":"https://api.github.com/users/agroppi/gists{/gist_id}","starred_url":"https://api.github.com/users/agroppi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/agroppi/subscriptions","organizations_url":"https://api.github.com/users/agroppi/orgs","repos_url":"https://api.github.com/users/agroppi/repos","events_url":"https://api.github.com/users/agroppi/events{/privacy}","received_events_url":"https://api.github.com/users/agroppi/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-05-23T13:20:36Z","updated_at":"2018-05-24T01:19:57Z","closed_at":null,"author_association":"NONE","body":"I have a draft assembly in scaffolds (61)\r\nWith the help of genetics markers I have ordered these scaffolds.\r\nThe results generated by the script I have used is a agp file.\r\n\r\nI want to use genGenomeFromAGP to construct the draft genome in linkage groups (chromosomes).\r\n\r\nBut I have a doubt about the input files needed as described in `genGenomeFromAGP --help`\r\n\r\nIs this command line correct ? : \r\n\r\n`genGenomeFromAGP  -f 4 -F mylogfile.log -m 1 -i scaffolds.fasta -I ordered_scaffolds.agp -o chomosome_assembly.fasta`\r\n\r\nThanks\r\n"},"comment":{"url":"https://api.github.com/repos/csiro-crop-informatics/biokanga/issues/comments/391556991","html_url":"https://github.com/csiro-crop-informatics/biokanga/issues/13#issuecomment-391556991","issue_url":"https://api.github.com/repos/csiro-crop-informatics/biokanga/issues/13","id":391556991,"user":{"login":"ste69r","id":2888728,"avatar_url":"https://avatars3.githubusercontent.com/u/2888728?v=4","gravatar_id":"","url":"https://api.github.com/users/ste69r","html_url":"https://github.com/ste69r","followers_url":"https://api.github.com/users/ste69r/followers","following_url":"https://api.github.com/users/ste69r/following{/other_user}","gists_url":"https://api.github.com/users/ste69r/gists{/gist_id}","starred_url":"https://api.github.com/users/ste69r/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ste69r/subscriptions","organizations_url":"https://api.github.com/users/ste69r/orgs","repos_url":"https://api.github.com/users/ste69r/repos","events_url":"https://api.github.com/users/ste69r/events{/privacy}","received_events_url":"https://api.github.com/users/ste69r/received_events","type":"User","site_admin":false},"created_at":"2018-05-24T01:19:57Z","updated_at":"2018-05-24T01:19:57Z","author_association":"CONTRIBUTOR","body":"To generate a scaffolded assembly (could still be gaps dependent on the completeness of the components and associated types in your AGP ) from the component sequences in your <scaffolds.fasta> using <ordered_scaffolds.agp> then change '-m 1' to be '-m 0' .\r\n\r\n '-m 1' is only used when you have an AGP for the generated assembly and you wish to know the component names and start/end offsets of these components in the generated assembly. This is dependent on the generated assembly being derived from an <ordered_scaffolds.agp>. \r\nThe output, when using '-m 1' is a CSV file containing 4 fields -\r\n1)   The super contig name ( could be a chromosome or named sequence ) in the assembly\r\n2)   The component name\r\n3)   Starting offset of component in the super contig\r\n4)   Ending offset of component in the super contig\r\n\r\nPlease let us know if you have further questions.  \r\n\r\n"}}
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