{"action":"created","issue":{"url":"https://api.github.com/repos/COMBINE-lab/salmon/issues/57","repository_url":"https://api.github.com/repos/COMBINE-lab/salmon","labels_url":"https://api.github.com/repos/COMBINE-lab/salmon/issues/57/labels{/name}","comments_url":"https://api.github.com/repos/COMBINE-lab/salmon/issues/57/comments","events_url":"https://api.github.com/repos/COMBINE-lab/salmon/issues/57/events","html_url":"https://github.com/COMBINE-lab/salmon/issues/57","id":154209118,"number":57,"title":"v.low strandness reported wrt genomic alignment w/ RSeQC ","user":{"login":"pinin4fjords","id":5775915,"avatar_url":"https://avatars.githubusercontent.com/u/5775915?v=3","gravatar_id":"","url":"https://api.github.com/users/pinin4fjords","html_url":"https://github.com/pinin4fjords","followers_url":"https://api.github.com/users/pinin4fjords/followers","following_url":"https://api.github.com/users/pinin4fjords/following{/other_user}","gists_url":"https://api.github.com/users/pinin4fjords/gists{/gist_id}","starred_url":"https://api.github.com/users/pinin4fjords/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pinin4fjords/subscriptions","organizations_url":"https://api.github.com/users/pinin4fjords/orgs","repos_url":"https://api.github.com/users/pinin4fjords/repos","events_url":"https://api.github.com/users/pinin4fjords/events{/privacy}","received_events_url":"https://api.github.com/users/pinin4fjords/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2016-05-11T10:21:40Z","updated_at":"2016-05-11T15:49:00Z","closed_at":"2016-05-11T15:49:00Z","body":"Thanks for your work on Salmon- interesting tool!\r\n\r\nSo, I'm running Salmon, and comparing it with a more conventional genomic alignment with HISAT2. I have TruSeq stranded data, and if I run HISAT2 and check strandedness using RSeQC's 'infer_experiment.py' and an Ensembl GTF (this is rat data btw), I get >98% as I expect.\r\n\r\nHere's an example libFormatCounts.txt from running Salmon 0.6 with the same reads, and a FASTA reference combining Ensembl's cDNA and ncRNA files:\r\n\r\nExpected format: Library format { type:paired end, relative orientation:inward, strandedness:(antisense, sense) }\r\n\r\n```\r\n# of consistent alignments: 73805886\r\n# of inconsistent alignments: 34539736\r\n\r\n========\r\n---- counts for each format type ---\r\nLibrary format { type:single end, relative orientation:matching, strandedness:(sense, antisense) } : 0\r\nLibrary format { type:paired end, relative orientation:matching, strandedness:(sense, antisense) } : 0\r\nLibrary format { type:single end, relative orientation:outward, strandedness:(sense, antisense) } : 0\r\nLibrary format { type:paired end, relative orientation:outward, strandedness:(sense, antisense) } : 4578\r\nLibrary format { type:single end, relative orientation:inward, strandedness:(sense, antisense) } : 0\r\nLibrary format { type:paired end, relative orientation:inward, strandedness:(sense, antisense) } : 11494138\r\nLibrary format { type:single end, relative orientation:none, strandedness:(sense, antisense) } : 0\r\nLibrary format { type:paired end, relative orientation:none, strandedness:(sense, antisense) } : 0\r\nLibrary format { type:single end, relative orientation:matching, strandedness:(antisense, sense) } : 0\r\nLibrary format { type:paired end, relative orientation:matching, strandedness:(antisense, sense) } : 0\r\nLibrary format { type:single end, relative orientation:outward, strandedness:(antisense, sense) } : 0\r\nLibrary format { type:paired end, relative orientation:outward, strandedness:(antisense, sense) } : 64175\r\nLibrary format { type:single end, relative orientation:inward, strandedness:(antisense, sense) } : 0\r\nLibrary format { type:paired end, relative orientation:inward, strandedness:(antisense, sense) } : 73805886\r\nLibrary format { type:single end, relative orientation:none, strandedness:(antisense, sense) } : 0\r\nLibrary format { type:paired end, relative orientation:none, strandedness:(antisense, sense) } : 0\r\nLibrary format { type:single end, relative orientation:matching, strandedness:sense } : 0\r\nLibrary format { type:paired end, relative orientation:matching, strandedness:sense } : 525\r\nLibrary format { type:single end, relative orientation:outward, strandedness:sense } : 0\r\nLibrary format { type:paired end, relative orientation:outward, strandedness:sense } : 0\r\nLibrary format { type:single end, relative orientation:inward, strandedness:sense } : 0\r\nLibrary format { type:paired end, relative orientation:inward, strandedness:sense } : 0\r\nLibrary format { type:single end, relative orientation:none, strandedness:sense } : 12094116\r\nLibrary format { type:paired end, relative orientation:none, strandedness:sense } : 0\r\nLibrary format { type:single end, relative orientation:matching, strandedness:antisense } : 0\r\nLibrary format { type:paired end, relative orientation:matching, strandedness:antisense } : 6539\r\nLibrary format { type:single end, relative orientation:outward, strandedness:antisense } : 0\r\nLibrary format { type:paired end, relative orientation:outward, strandedness:antisense } : 0\r\nLibrary format { type:single end, relative orientation:inward, strandedness:antisense } : 0\r\nLibrary format { type:paired end, relative orientation:inward, strandedness:antisense } : 0\r\nLibrary format { type:single end, relative orientation:none, strandedness:antisense } : 10875665\r\nLibrary format { type:paired end, relative orientation:none, strandedness:antisense } : 0\r\nLibrary format { type:single end, relative orientation:matching, strandedness:unstranded } : 0\r\nLibrary format { type:paired end, relative orientation:matching, strandedness:unstranded } : 0\r\nLibrary format { type:single end, relative orientation:outward, strandedness:unstranded } : 0\r\nLibrary format { type:paired end, relative orientation:outward, strandedness:unstranded } : 0\r\nLibrary format { type:single end, relative orientation:inward, strandedness:unstranded } : 0\r\nLibrary format { type:paired end, relative orientation:inward, strandedness:unstranded } : 0\r\nLibrary format { type:single end, relative orientation:none, strandedness:unstranded } : 0\r\nLibrary format { type:paired end, relative orientation:none, strandedness:unstranded } : 0\r\n```\r\n\r\nAs you can see the data looks much less stranded here!\r\n\r\nIs this a feature of how Salmon is operating, or a problem with the FASTA reference? Is it something I should be concerned about?"},"comment":{"url":"https://api.github.com/repos/COMBINE-lab/salmon/issues/comments/218501851","html_url":"https://github.com/COMBINE-lab/salmon/issues/57#issuecomment-218501851","issue_url":"https://api.github.com/repos/COMBINE-lab/salmon/issues/57","id":218501851,"user":{"login":"rob-p","id":361470,"avatar_url":"https://avatars.githubusercontent.com/u/361470?v=3","gravatar_id":"","url":"https://api.github.com/users/rob-p","html_url":"https://github.com/rob-p","followers_url":"https://api.github.com/users/rob-p/followers","following_url":"https://api.github.com/users/rob-p/following{/other_user}","gists_url":"https://api.github.com/users/rob-p/gists{/gist_id}","starred_url":"https://api.github.com/users/rob-p/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rob-p/subscriptions","organizations_url":"https://api.github.com/users/rob-p/orgs","repos_url":"https://api.github.com/users/rob-p/repos","events_url":"https://api.github.com/users/rob-p/events{/privacy}","received_events_url":"https://api.github.com/users/rob-p/received_events","type":"User","site_admin":false},"created_at":"2016-05-11T15:49:00Z","updated_at":"2016-05-11T15:49:00Z","body":"I'm closing this issue since it's addressed [here](https://groups.google.com/forum/#!topic/sailfish-users/JNO_Q5ULpe4).  However, the action item is to modify (or augment) the manner in which consistent and inconsistent mappings are reported."}}