{"action":"created","issue":{"url":"https://api.github.com/repos/eturro/mmseq/issues/13","repository_url":"https://api.github.com/repos/eturro/mmseq","labels_url":"https://api.github.com/repos/eturro/mmseq/issues/13/labels{/name}","comments_url":"https://api.github.com/repos/eturro/mmseq/issues/13/comments","events_url":"https://api.github.com/repos/eturro/mmseq/issues/13/events","html_url":"https://github.com/eturro/mmseq/issues/13","id":155103225,"number":13,"title":"how to supply regex for bam2hits with single sequence name?","user":{"login":"n-long","id":8417928,"avatar_url":"https://avatars.githubusercontent.com/u/8417928?v=3","gravatar_id":"","url":"https://api.github.com/users/n-long","html_url":"https://github.com/n-long","followers_url":"https://api.github.com/users/n-long/followers","following_url":"https://api.github.com/users/n-long/following{/other_user}","gists_url":"https://api.github.com/users/n-long/gists{/gist_id}","starred_url":"https://api.github.com/users/n-long/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/n-long/subscriptions","organizations_url":"https://api.github.com/users/n-long/orgs","repos_url":"https://api.github.com/users/n-long/repos","events_url":"https://api.github.com/users/n-long/events{/privacy}","received_events_url":"https://api.github.com/users/n-long/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2016-05-16T19:32:15Z","updated_at":"2016-05-16T21:31:14Z","closed_at":null,"body":"Hello,\r\n\r\nAll of my sequence headers share a single word format such as GENE_strain. I added a gene and transcript identifier originally, but my read mapping failed when using '--fullref' argument to bowtie1 using tophat (you can add all of the arguments at around line 2349 in the tophat executable). I had to go that route since using bowtie as provided in the manual was not producing a proper SAM alignment format, despite correct flags. Anyway, all my gene and transcript identifiers are 1:1 anyway, but I cannot figure out the regex pattern to make bam2hits assign the sequence header to both identifiers.\r\n\r\nI've gotten this far but I can't get past a segfault. \r\nbam2hits -m \\\"(\\S+)\\\" 1 1\r\n\r\nThanks.\r\n\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/eturro/mmseq/issues/comments/219554495","html_url":"https://github.com/eturro/mmseq/issues/13#issuecomment-219554495","issue_url":"https://api.github.com/repos/eturro/mmseq/issues/13","id":219554495,"user":{"login":"eturro","id":4404752,"avatar_url":"https://avatars.githubusercontent.com/u/4404752?v=3","gravatar_id":"","url":"https://api.github.com/users/eturro","html_url":"https://github.com/eturro","followers_url":"https://api.github.com/users/eturro/followers","following_url":"https://api.github.com/users/eturro/following{/other_user}","gists_url":"https://api.github.com/users/eturro/gists{/gist_id}","starred_url":"https://api.github.com/users/eturro/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/eturro/subscriptions","organizations_url":"https://api.github.com/users/eturro/orgs","repos_url":"https://api.github.com/users/eturro/repos","events_url":"https://api.github.com/users/eturro/events{/privacy}","received_events_url":"https://api.github.com/users/eturro/received_events","type":"User","site_admin":false},"created_at":"2016-05-16T21:31:14Z","updated_at":"2016-05-16T21:31:14Z","body":"> bowtie as provided in the manual was not producing a proper SAM alignment format, despite correct flags\n> \nHi,\nI think we should get to the bottom of this first as tophat is designed for alignment to the genome (with spliced alignments), not alignment to a transcriptome.\n\nWhat exactly is the problem with running bowtie1? Could you expand on this please ? I've been using it for years without a problem.\n\nMany thanks\n\n\n> On 16 May 2016, at 20:32, Nick Long <notifications@github.com> wrote:\n> \n> Hello,\n> \n> All of my sequence headers share a single word format such as GENE_strain. I added a gene and transcript identifier originally, but my read mapping failed when using '--fullref' argument to bowtie1 using tophat (you can add all of the arguments at around line 2349 in the tophat executable). I had to go that route since using bowtie as provided in the manual was not producing a proper SAM alignment format, despite correct flags. Anyway, all my gene and transcript identifiers would be 1:1 anyway, but I cannot figure out the regex pattern to make bam2hits accept the sequence header to both.\n> \n> I've gotten this far but I can't get past a segfault. \n> bam2hits -m \\\"(\\S+)\\\" 1 1\n> \n> Thanks.\n> \n> —\n> You are receiving this because you are subscribed to this thread.\n> Reply to this email directly or view it on GitHub <https://github.com/eturro/mmseq/issues/13>\n\n"}}