{"action":"created","issue":{"url":"https://api.github.com/repos/cerebis/meta-sweeper/issues/40","repository_url":"https://api.github.com/repos/cerebis/meta-sweeper","labels_url":"https://api.github.com/repos/cerebis/meta-sweeper/issues/40/labels{/name}","comments_url":"https://api.github.com/repos/cerebis/meta-sweeper/issues/40/comments","events_url":"https://api.github.com/repos/cerebis/meta-sweeper/issues/40/events","html_url":"https://github.com/cerebis/meta-sweeper/issues/40","id":175393885,"number":40,"title":"BWA MEM mapping can produce no mapped reads to some contigs","user":{"login":"cerebis","id":6006667,"avatar_url":"https://avatars.githubusercontent.com/u/6006667?v=3","gravatar_id":"","url":"https://api.github.com/users/cerebis","html_url":"https://github.com/cerebis","followers_url":"https://api.github.com/users/cerebis/followers","following_url":"https://api.github.com/users/cerebis/following{/other_user}","gists_url":"https://api.github.com/users/cerebis/gists{/gist_id}","starred_url":"https://api.github.com/users/cerebis/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cerebis/subscriptions","organizations_url":"https://api.github.com/users/cerebis/orgs","repos_url":"https://api.github.com/users/cerebis/repos","events_url":"https://api.github.com/users/cerebis/events{/privacy}","received_events_url":"https://api.github.com/users/cerebis/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/cerebis/meta-sweeper/labels/question","name":"question","color":"cc317c"},{"url":"https://api.github.com/repos/cerebis/meta-sweeper/labels/Research","name":"Research","color":"fbca04"}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2016-09-07T01:48:56Z","updated_at":"2016-09-07T02:54:45Z","closed_at":null,"body":"Using BWA MEM to map WGS reads to metagenomic contigs, it is possible to find no reads mapping to a small number of short contigs. This then results in inferring contig coverages of zero and an inability to observe SNV from pileups generated from these BAM files.\r\n\r\nUsing LAST to align an example contig to the originating set of community sequences, full alignments are reported for all 8 taxa in the community. However, all possess single nucleotide gaps (from 5 to 32 SNV) that must exceed the constraints of BWA.\r\n\r\nExperimenting with constraints in BWA MEM, removing penalties for clipping and unpaired reads has a significant impact. Skipping mate rescue and pairing also results in reads being mapped, although less."},"comment":{"url":"https://api.github.com/repos/cerebis/meta-sweeper/issues/comments/245160578","html_url":"https://github.com/cerebis/meta-sweeper/issues/40#issuecomment-245160578","issue_url":"https://api.github.com/repos/cerebis/meta-sweeper/issues/40","id":245160578,"user":{"login":"koadman","id":242390,"avatar_url":"https://avatars.githubusercontent.com/u/242390?v=3","gravatar_id":"","url":"https://api.github.com/users/koadman","html_url":"https://github.com/koadman","followers_url":"https://api.github.com/users/koadman/followers","following_url":"https://api.github.com/users/koadman/following{/other_user}","gists_url":"https://api.github.com/users/koadman/gists{/gist_id}","starred_url":"https://api.github.com/users/koadman/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/koadman/subscriptions","organizations_url":"https://api.github.com/users/koadman/orgs","repos_url":"https://api.github.com/users/koadman/repos","events_url":"https://api.github.com/users/koadman/events{/privacy}","received_events_url":"https://api.github.com/users/koadman/received_events","type":"User","site_admin":false},"created_at":"2016-09-07T02:54:45Z","updated_at":"2016-09-07T02:54:45Z","body":"hmm, i'm not sure i know enough about how samtools pileup is calculating coverage to have a sense for what to expect in the coverage distribution, assuming we are still talking about closely related strains? If not then yes, I agree there should be distinct peaks, but if closely related, mapping uncertainty seems like it could come into play and if pileup decides to spread 1 read among 3 equally good references then perhaps the coverage distribution might not have peaks anymore?"}}
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