{"action":"created","issue":{"url":"https://api.github.com/repos/UofTCoders/studyGroup/issues/7","labels_url":"https://api.github.com/repos/UofTCoders/studyGroup/issues/7/labels{/name}","comments_url":"https://api.github.com/repos/UofTCoders/studyGroup/issues/7/comments","events_url":"https://api.github.com/repos/UofTCoders/studyGroup/issues/7/events","html_url":"https://github.com/UofTCoders/studyGroup/issues/7","id":88509860,"number":7,"title":"Bioinformatics topic ideas","user":{"login":"mbonsma","id":5651370,"avatar_url":"https://avatars.githubusercontent.com/u/5651370?v=3","gravatar_id":"","url":"https://api.github.com/users/mbonsma","html_url":"https://github.com/mbonsma","followers_url":"https://api.github.com/users/mbonsma/followers","following_url":"https://api.github.com/users/mbonsma/following{/other_user}","gists_url":"https://api.github.com/users/mbonsma/gists{/gist_id}","starred_url":"https://api.github.com/users/mbonsma/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mbonsma/subscriptions","organizations_url":"https://api.github.com/users/mbonsma/orgs","repos_url":"https://api.github.com/users/mbonsma/repos","events_url":"https://api.github.com/users/mbonsma/events{/privacy}","received_events_url":"https://api.github.com/users/mbonsma/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":18,"created_at":"2015-06-15T18:54:57Z","updated_at":"2015-06-20T18:48:51Z","closed_at":null,"body":"Suggestions and ideas for topics we'd like to see covered at some point. This thread is for bioinformatics-related topics, or things that people working with genetic data might find useful. Posting a suggestion does not lock you in to presenting on that topic."},"comment":{"url":"https://api.github.com/repos/UofTCoders/studyGroup/issues/comments/113803920","html_url":"https://github.com/UofTCoders/studyGroup/issues/7#issuecomment-113803920","issue_url":"https://api.github.com/repos/UofTCoders/studyGroup/issues/7","id":113803920,"user":{"login":"MattStata","id":12849438,"avatar_url":"https://avatars.githubusercontent.com/u/12849438?v=3","gravatar_id":"","url":"https://api.github.com/users/MattStata","html_url":"https://github.com/MattStata","followers_url":"https://api.github.com/users/MattStata/followers","following_url":"https://api.github.com/users/MattStata/following{/other_user}","gists_url":"https://api.github.com/users/MattStata/gists{/gist_id}","starred_url":"https://api.github.com/users/MattStata/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/MattStata/subscriptions","organizations_url":"https://api.github.com/users/MattStata/orgs","repos_url":"https://api.github.com/users/MattStata/repos","events_url":"https://api.github.com/users/MattStata/events{/privacy}","received_events_url":"https://api.github.com/users/MattStata/received_events","type":"User","site_admin":false},"created_at":"2015-06-20T18:48:51Z","updated_at":"2015-06-20T18:48:51Z","body":"BLAT actually works quite well for mapping reads, and can be really fast with the right settings and run in parallel with gnu parallel.  I've used it quite a bit for that.\r\n\r\nMy pipeline, which I'm still refining, is something like this:\r\n\r\n-Multiple assemblies (Trinity, IDBA, SOAPDeNovo-Trans) combined\r\n-Predict ORFs with EMBOSS \"getorf\" and take the three longest per assembled transcript, above a certain minimum length threshold, using a Python script (this of course introduces a lot of spurious ORFs, but they're filtered out over the next steps).\r\n-Remove duplicate ORFs with another Python script\r\n-Merge highly similar ORFs and take a single representative using CD-HIT in order to reduce redundancy\r\n-BLAST the ORFs for my two species against each other and take reciprocal best hits to further reduce redundancy\r\n-BLAST what remains against selected genomes in the Phytozome v10.2, and eliminate anything without a good match, to remove totally spurious ORFs that might remain\r\n-Cluster the results of the two BLAST comparisons using MCL in order to group my assemblies with their orthologs in other species for functional annotation\r\n\r\nBasically this is all aimed at getting a good set of pairwise orthologs with predicted function, so that I can then do further downstream analysis with interspecific hybrids of these two species.  But as I mentioned, we also intend to eventually sequence the genomes of the two parent species and so would like to get a rough idea of the degree of heterozygosity so as to decide whether we need to self a few more times before starting sequencing.  So I'd like to see what SNPs exist in my coding regions (particularly percentage of SNPs at synonymous sites, which should be a reasonable approximation of SNPs for the other neutral parts of the genome) for each species.\r\n\r\nPAGAN sounds interesting, but I don't see how it fits my problem -- were you suggesting it just as an alternative to BLAT?"}}