{"action":"created","issue":{"url":"https://api.github.com/repos/PacificBiosciences/pbsmrtpipe/issues/498","repository_url":"https://api.github.com/repos/PacificBiosciences/pbsmrtpipe","labels_url":"https://api.github.com/repos/PacificBiosciences/pbsmrtpipe/issues/498/labels{/name}","comments_url":"https://api.github.com/repos/PacificBiosciences/pbsmrtpipe/issues/498/comments","events_url":"https://api.github.com/repos/PacificBiosciences/pbsmrtpipe/issues/498/events","html_url":"https://github.com/PacificBiosciences/pbsmrtpipe/issues/498","id":173470212,"number":498,"title":"What is the correlation between pbsmrtpip and smrtanalysis protocols? ","user":{"login":"yech1990","id":5415510,"avatar_url":"https://avatars.githubusercontent.com/u/5415510?v=3","gravatar_id":"","url":"https://api.github.com/users/yech1990","html_url":"https://github.com/yech1990","followers_url":"https://api.github.com/users/yech1990/followers","following_url":"https://api.github.com/users/yech1990/following{/other_user}","gists_url":"https://api.github.com/users/yech1990/gists{/gist_id}","starred_url":"https://api.github.com/users/yech1990/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/yech1990/subscriptions","organizations_url":"https://api.github.com/users/yech1990/orgs","repos_url":"https://api.github.com/users/yech1990/repos","events_url":"https://api.github.com/users/yech1990/events{/privacy}","received_events_url":"https://api.github.com/users/yech1990/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2016-08-26T14:44:26Z","updated_at":"2016-08-26T20:52:23Z","closed_at":null,"body":"I notice that `pbsmrtpipe` protocols are named as \\*\\_sa3_ds\\_\\*, where 'sa3' and 'ds' look like abbreviations.\r\n> I have two questions.\r\n\r\n1. Whether 'sa3' is short for `Smrt Analysis 3.0` ?\r\n2. The protocols in `smrtanalysis-2.3.0` don't have 'sa3' in there file names. Does it means the `smrtanalysis` 2.3.0 version use the old protocols?  \r\n\r\n```bash\r\n$ ls ./smrtanalysis/install/smrtanalysis_2.3.0.140936/common/protocols\r\n\r\napplications.xml                RS_BridgeMapper.1.xml\r\nassembly                        RS_HGAP_Assembly.2.xml\r\nBAM_Resequencing_Beta.1.xml     RS_HGAP_Assembly.3.xml\r\nbarcode                         RS_IsoSeq.1.xml\r\nconsensus                       RS_Long_Amplicon_Analysis.1.xml\r\ncontrol                         RS_Minor_Variant.1.xml\r\nfiltering                       RS_Modification_and_Motif_Analysis.1.xml\r\nisoseq                          RS_Modification_Detection.1.xml\r\nmapping                         RS_PreAssembler.2.xml\r\nNew_Protocol_Assembly.template  RS_ReadsOfInsert.1.xml\r\nNew_Protocol.template           RS_ReadsOfInsert_Mapping.1.xml\r\npostprocessing                  RS_Resequencing.1.xml\r\npreprocessing                   RS_Resequencing_Barcode.1.xml\r\nreferenceuploader               RS_Site_Acceptance_Test.1.xml\r\nRS_AHA_Scaffolding.1.xml        RS_Subreads.1.xml\r\n```\r\n\r\n\r\n```bash\r\n$ pbsmrtpipe show-templates  | grep sa3\r\n\r\n 37. RS movie Align                                                        0.1.0 pbsmrtpipe.pipelines.sa3_align\r\n 38. SubreadSet Mapping                                                    0.1.0 pbsmrtpipe.pipelines.sa3_ds_align\r\n 39. Unrolled Template SubreadSet Mapping                                  0.1.0 pbsmrtpipe.pipelines.sa3_ds_align_unrolled\r\n 40. Barcoding                                                             0.1.0 pbsmrtpipe.pipelines.sa3_ds_barcode\r\n 41. CCS with Barcoding                                                    0.1.0 pbsmrtpipe.pipelines.sa3_ds_barcode_ccs\r\n 42. LAA with Barcoding                                                    0.2.0 pbsmrtpipe.pipelines.sa3_ds_barcode_laa\r\n 43. Circular Consensus Sequences (CCS 2)                                  0.1.0 pbsmrtpipe.pipelines.sa3_ds_ccs\r\n 44. CCS Mapping                                                           0.1.0 pbsmrtpipe.pipelines.sa3_ds_ccs_align\r\n 45. Convert FASTA to ReferenceSet                                         0.1.0 pbsmrtpipe.pipelines.sa3_ds_fasta_to_reference\r\n...\r\n```"},"comment":{"url":"https://api.github.com/repos/PacificBiosciences/pbsmrtpipe/issues/comments/242848545","html_url":"https://github.com/PacificBiosciences/pbsmrtpipe/issues/498#issuecomment-242848545","issue_url":"https://api.github.com/repos/PacificBiosciences/pbsmrtpipe/issues/498","id":242848545,"user":{"login":"evolvedmicrobe","id":1330626,"avatar_url":"https://avatars.githubusercontent.com/u/1330626?v=3","gravatar_id":"","url":"https://api.github.com/users/evolvedmicrobe","html_url":"https://github.com/evolvedmicrobe","followers_url":"https://api.github.com/users/evolvedmicrobe/followers","following_url":"https://api.github.com/users/evolvedmicrobe/following{/other_user}","gists_url":"https://api.github.com/users/evolvedmicrobe/gists{/gist_id}","starred_url":"https://api.github.com/users/evolvedmicrobe/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/evolvedmicrobe/subscriptions","organizations_url":"https://api.github.com/users/evolvedmicrobe/orgs","repos_url":"https://api.github.com/users/evolvedmicrobe/repos","events_url":"https://api.github.com/users/evolvedmicrobe/events{/privacy}","received_events_url":"https://api.github.com/users/evolvedmicrobe/received_events","type":"User","site_admin":false},"created_at":"2016-08-26T20:52:22Z","updated_at":"2016-08-26T20:52:22Z","body":"@yech1990 - If you would like, it is likely easier to run CCS2 directly from the command line, rather than piping it through the framework.  You can compile a version of it here: https://github.com/PacificBiosciences/unanimity"}}
{"actor":{"display_login":"evolvedmicrobe"}}