{"action":"created","issue":{"url":"https://api.github.com/repos/raunaq-m/MLEHaplo/issues/2","repository_url":"https://api.github.com/repos/raunaq-m/MLEHaplo","labels_url":"https://api.github.com/repos/raunaq-m/MLEHaplo/issues/2/labels{/name}","comments_url":"https://api.github.com/repos/raunaq-m/MLEHaplo/issues/2/comments","events_url":"https://api.github.com/repos/raunaq-m/MLEHaplo/issues/2/events","html_url":"https://github.com/raunaq-m/MLEHaplo/issues/2","id":156431362,"number":2,"title":"How to make FASTA file from paired end FASTQ?","user":{"login":"sdwfrost","id":2164195,"avatar_url":"https://avatars.githubusercontent.com/u/2164195?v=3","gravatar_id":"","url":"https://api.github.com/users/sdwfrost","html_url":"https://github.com/sdwfrost","followers_url":"https://api.github.com/users/sdwfrost/followers","following_url":"https://api.github.com/users/sdwfrost/following{/other_user}","gists_url":"https://api.github.com/users/sdwfrost/gists{/gist_id}","starred_url":"https://api.github.com/users/sdwfrost/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sdwfrost/subscriptions","organizations_url":"https://api.github.com/users/sdwfrost/orgs","repos_url":"https://api.github.com/users/sdwfrost/repos","events_url":"https://api.github.com/users/sdwfrost/events{/privacy}","received_events_url":"https://api.github.com/users/sdwfrost/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2016-05-24T06:47:09Z","updated_at":"2016-05-24T16:03:49Z","closed_at":null,"body":"In the step\r\n\r\n```\r\n perl construct_graph.pl \"fastafile\" \"kmerfile\" \"threshold\" \"graphfile\" \"s\"\r\n```\r\n\r\nOne has to make a single FASTA file from paired end FASTQ. It appears that you have to run\r\n\r\n```\r\nperl fastqtofasta.pl <read file>\r\n```\r\n\r\nfor each read, and then cat...is this OK (given that the reverse read is in the opposite direction)"},"comment":{"url":"https://api.github.com/repos/raunaq-m/MLEHaplo/issues/comments/221320110","html_url":"https://github.com/raunaq-m/MLEHaplo/issues/2#issuecomment-221320110","issue_url":"https://api.github.com/repos/raunaq-m/MLEHaplo/issues/2","id":221320110,"user":{"login":"raunaq-m","id":16708269,"avatar_url":"https://avatars.githubusercontent.com/u/16708269?v=3","gravatar_id":"","url":"https://api.github.com/users/raunaq-m","html_url":"https://github.com/raunaq-m","followers_url":"https://api.github.com/users/raunaq-m/followers","following_url":"https://api.github.com/users/raunaq-m/following{/other_user}","gists_url":"https://api.github.com/users/raunaq-m/gists{/gist_id}","starred_url":"https://api.github.com/users/raunaq-m/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/raunaq-m/subscriptions","organizations_url":"https://api.github.com/users/raunaq-m/orgs","repos_url":"https://api.github.com/users/raunaq-m/repos","events_url":"https://api.github.com/users/raunaq-m/events{/privacy}","received_events_url":"https://api.github.com/users/raunaq-m/received_events","type":"User","site_admin":false},"created_at":"2016-05-24T16:03:49Z","updated_at":"2016-05-24T16:03:49Z","body":"Yes. One can use cat to combine the two fasta files. The graph stores both forward and reverse kmers from every read, so the reverse orientation is taken care of. \r\n"}}
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