{"action":"created","issue":{"url":"https://api.github.com/repos/pnnl/atlas/issues/87","repository_url":"https://api.github.com/repos/pnnl/atlas","labels_url":"https://api.github.com/repos/pnnl/atlas/issues/87/labels{/name}","comments_url":"https://api.github.com/repos/pnnl/atlas/issues/87/comments","events_url":"https://api.github.com/repos/pnnl/atlas/issues/87/events","html_url":"https://github.com/pnnl/atlas/issues/87","id":295069052,"number":87,"title":" taxonomic profiles","user":{"login":"SilasK","id":7523034,"avatar_url":"https://avatars3.githubusercontent.com/u/7523034?v=4","gravatar_id":"","url":"https://api.github.com/users/SilasK","html_url":"https://github.com/SilasK","followers_url":"https://api.github.com/users/SilasK/followers","following_url":"https://api.github.com/users/SilasK/following{/other_user}","gists_url":"https://api.github.com/users/SilasK/gists{/gist_id}","starred_url":"https://api.github.com/users/SilasK/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/SilasK/subscriptions","organizations_url":"https://api.github.com/users/SilasK/orgs","repos_url":"https://api.github.com/users/SilasK/repos","events_url":"https://api.github.com/users/SilasK/events{/privacy}","received_events_url":"https://api.github.com/users/SilasK/received_events","type":"User","site_admin":false},"labels":[{"id":491786088,"url":"https://api.github.com/repos/pnnl/atlas/labels/question","name":"question","color":"cc317c","default":true}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":6,"created_at":"2018-02-07T09:45:35Z","updated_at":"2018-02-07T16:25:49Z","closed_at":null,"author_association":"COLLABORATOR","body":"Dear Silas,\r\n\r\nLast time, I consulted you about the taxonomic and functional profiling for metagenomic data. After check the several papers and blocks, I want to try metaphlan2 and humann2 to get taxonomic and functional profile, respectively. I am not sure whether you are familiar with the two pipeline, my question will be very general before running the two pipeline.\r\n\r\nAll my data is paired-end data, while it appears that both metaphlan2 and humann2 do not support paired-end analysis. For this step, I would like to use atlas to merge each to to on paired fastq file. In this case, shall what should I specify in atlas assemble -until?\r\n\r\nIn addition, I am not sure which fastq is the best for taxonomic and functional profile, shall I use the data generated after 1) quality control (quality controlled reads) or 2) assembly? I don't have clue but feel that it will be better to use the merged fastq file at least after quality control. Can you give me more instruction in this point? To get this file, what parameter shall I further specify in atlas assemble flow?\r\n\r\nLooking forward to hearing from you.\r\n\r\nThank you and best regards,\r\n\r\ncam315"},"comment":{"url":"https://api.github.com/repos/pnnl/atlas/issues/comments/363824865","html_url":"https://github.com/pnnl/atlas/issues/87#issuecomment-363824865","issue_url":"https://api.github.com/repos/pnnl/atlas/issues/87","id":363824865,"user":{"login":"SilasK","id":7523034,"avatar_url":"https://avatars3.githubusercontent.com/u/7523034?v=4","gravatar_id":"","url":"https://api.github.com/users/SilasK","html_url":"https://github.com/SilasK","followers_url":"https://api.github.com/users/SilasK/followers","following_url":"https://api.github.com/users/SilasK/following{/other_user}","gists_url":"https://api.github.com/users/SilasK/gists{/gist_id}","starred_url":"https://api.github.com/users/SilasK/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/SilasK/subscriptions","organizations_url":"https://api.github.com/users/SilasK/orgs","repos_url":"https://api.github.com/users/SilasK/repos","events_url":"https://api.github.com/users/SilasK/events{/privacy}","received_events_url":"https://api.github.com/users/SilasK/received_events","type":"User","site_admin":false},"created_at":"2018-02-07T16:25:49Z","updated_at":"2018-02-07T16:25:49Z","author_association":"COLLABORATOR","body":"I don't know, I see there no comparable id. taxonomy would be eventually possible, but it's not defined for all genes. \r\n"}}
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