{"action":"created","issue":{"url":"https://api.github.com/repos/marcelm/cutadapt/issues/200","repository_url":"https://api.github.com/repos/marcelm/cutadapt","labels_url":"https://api.github.com/repos/marcelm/cutadapt/issues/200/labels{/name}","comments_url":"https://api.github.com/repos/marcelm/cutadapt/issues/200/comments","events_url":"https://api.github.com/repos/marcelm/cutadapt/issues/200/events","html_url":"https://github.com/marcelm/cutadapt/issues/200","id":156939729,"number":200,"title":"how to trim anchored multiple sequences","user":{"login":"danshu","id":9067238,"avatar_url":"https://avatars.githubusercontent.com/u/9067238?v=3","gravatar_id":"","url":"https://api.github.com/users/danshu","html_url":"https://github.com/danshu","followers_url":"https://api.github.com/users/danshu/followers","following_url":"https://api.github.com/users/danshu/following{/other_user}","gists_url":"https://api.github.com/users/danshu/gists{/gist_id}","starred_url":"https://api.github.com/users/danshu/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/danshu/subscriptions","organizations_url":"https://api.github.com/users/danshu/orgs","repos_url":"https://api.github.com/users/danshu/repos","events_url":"https://api.github.com/users/danshu/events{/privacy}","received_events_url":"https://api.github.com/users/danshu/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2016-05-26T09:19:11Z","updated_at":"2016-05-26T13:16:08Z","closed_at":null,"body":"Hello,\r\n\r\nI want to trim 3' anchored adapter sequences of different length, e.g.\r\n>f1\r\nAGATCGGAAGAGCACA$\r\n>f2\r\nAGATCGGAAGAGCAC$\r\n>f3\r\nAGATCGGAAGAGCA$\r\n>f4\r\nAGATCGGAAGAGC$\r\n\r\nI saved the adapter sequences in fasta files and used -a file:forward_adapters.fasta -A file:reverse_adapters.fasta in the command since I was trimming paired end data. I added \"$\" at the end of adapter sequences to only trim anchored 3' adapter sequences. \r\n\r\nI tested it on some sample data, however, I found that the \"$\" seems didn't work, i.e. reads with internal adapter (***ADAPTER****) will also be trimmed. So it it because that \"$\" is not supported in the file?\r\nAny one can help?\r\n\r\nBest,\r\nQuan"},"comment":{"url":"https://api.github.com/repos/marcelm/cutadapt/issues/comments/221867300","html_url":"https://github.com/marcelm/cutadapt/issues/200#issuecomment-221867300","issue_url":"https://api.github.com/repos/marcelm/cutadapt/issues/200","id":221867300,"user":{"login":"marcelm","id":724864,"avatar_url":"https://avatars.githubusercontent.com/u/724864?v=3","gravatar_id":"","url":"https://api.github.com/users/marcelm","html_url":"https://github.com/marcelm","followers_url":"https://api.github.com/users/marcelm/followers","following_url":"https://api.github.com/users/marcelm/following{/other_user}","gists_url":"https://api.github.com/users/marcelm/gists{/gist_id}","starred_url":"https://api.github.com/users/marcelm/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/marcelm/subscriptions","organizations_url":"https://api.github.com/users/marcelm/orgs","repos_url":"https://api.github.com/users/marcelm/repos","events_url":"https://api.github.com/users/marcelm/events{/privacy}","received_events_url":"https://api.github.com/users/marcelm/received_events","type":"User","site_admin":false},"created_at":"2016-05-26T13:16:08Z","updated_at":"2016-05-26T13:16:08Z","body":"Hi, yes, the `$` is supported even if you use the `file:` syntax. You are right, the error rate and indels being allowed by default explains what you saw.\r\n\r\nThere is [a trick mentioned in the 'recipes' section of the documentation](http://cutadapt.readthedocs.io/en/stable/recipes.html#forcing-matches-to-be-at-the-end-of-the-read) that you can use: Just specify `-a ADAPTERXXX` with a few `X` characters in the end. These do not match any base, and in this way you can avoid internal matches. Just make sure that there are more `X` characters than the length of the adapter times the error rate."}}
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