{"action":"created","issue":{"url":"https://api.github.com/repos/milaboratory/mixcr/issues/471","repository_url":"https://api.github.com/repos/milaboratory/mixcr","labels_url":"https://api.github.com/repos/milaboratory/mixcr/issues/471/labels{/name}","comments_url":"https://api.github.com/repos/milaboratory/mixcr/issues/471/comments","events_url":"https://api.github.com/repos/milaboratory/mixcr/issues/471/events","html_url":"https://github.com/milaboratory/mixcr/issues/471","id":391653770,"node_id":"MDU6SXNzdWUzOTE2NTM3NzA=","number":471,"title":"mixcr kaligner","user":{"login":"ibseq","id":33546691,"node_id":"MDQ6VXNlcjMzNTQ2Njkx","avatar_url":"https://avatars0.githubusercontent.com/u/33546691?v=4","gravatar_id":"","url":"https://api.github.com/users/ibseq","html_url":"https://github.com/ibseq","followers_url":"https://api.github.com/users/ibseq/followers","following_url":"https://api.github.com/users/ibseq/following{/other_user}","gists_url":"https://api.github.com/users/ibseq/gists{/gist_id}","starred_url":"https://api.github.com/users/ibseq/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ibseq/subscriptions","organizations_url":"https://api.github.com/users/ibseq/orgs","repos_url":"https://api.github.com/users/ibseq/repos","events_url":"https://api.github.com/users/ibseq/events{/privacy}","received_events_url":"https://api.github.com/users/ibseq/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":21,"created_at":"2018-12-17T10:45:39Z","updated_at":"2018-12-19T10:48:50Z","closed_at":null,"author_association":"NONE","body":"hi\r\ni ran mixcr with and without -p kaligner2 and got:\r\nWITH:\r\nAnalysis Date: Mon Dec 17 10:38:55 GMT 2018\r\nInput file(s): IB-031218-1_S1_L001_R1_001.TRIM.fastq.gz,IB-031218-1_S1_L001_R2_001.fastq.gz\r\nOutput file(s): alignments.vdjca\r\nVersion: 2.1.10; built=Fri Mar 30 15:59:50 BST 2018; rev=87f92f5; lib=repseqio.v1.5\r\nCommand line arguments: align --species hs -p kaligner2 -c IGH --report report.txt IB-031218-1_S1_L001_R1_001.TRIM.fastq.gz IB-031218-1_S1_L001_R2_001.fastq.gz alignments.vdjca\r\nAnalysis time: 8.45s\r\nTotal sequencing reads: 83857\r\nSuccessfully aligned reads: 4 (0%)\r\nAlignment failed, no hits (not TCR/IG?): 60213 (71.8%)\r\nAlignment failed because of absence of V hits: 8 (0.01%)\r\nAlignment failed because of absence of J hits: 23632 (28.18%)\r\nOverlapped: 4258 (5.08%)\r\nOverlapped and aligned: 0 (0%)\r\nAlignment-aided overlaps: 0 (�%)\r\nOverlapped and not aligned: 4258 (5.08%)\r\nIGH chains: 4 (100%)\r\n\r\nWITHOUT:\r\nAnalysis Date: Mon Dec 17 10:21:33 GMT 2018\r\nInput file(s): IB-031218-1_S1_L001_R1_001.TRIM.fastq.gz,IB-031218-1_S1_L001_R2_001.fastq.gz\r\nOutput file(s): alignmentsH.vdjca\r\nVersion: 2.1.10; built=Fri Mar 30 15:59:50 BST 2018; rev=87f92f5; lib=repseqio.v1.5\r\nCommand line arguments: align --species hs -c IGH --report reportH.txt IB-031218-1_S1_L001_R1_001.TRIM.fastq.gz IB-031218-1_S1_L001_R2_001.fastq.gz alignmentsH.vdjca\r\nAnalysis time: 8.49s\r\nTotal sequencing reads: 83857\r\nSuccessfully aligned reads: 9 (0.01%)\r\nPaired-end alignment conflicts eliminated: 1 (0%)\r\nAlignment failed, no hits (not TCR/IG?): 11996 (14.31%)\r\nAlignment failed because of absence of V hits: 126 (0.15%)\r\nAlignment failed because of absence of J hits: 71556 (85.33%)\r\nNo target with both V and J alignments: 53 (0.06%)\r\nAlignment failed because of low total score: 117 (0.14%)\r\nOverlapped: 4258 (5.08%)\r\nOverlapped and aligned: 0 (0%)\r\nAlignment-aided overlaps: 0 (�%)\r\nOverlapped and not aligned: 4258 (5.08%)\r\nIGH chains: 9 (100%)\r\n\r\nwhat is the difference and which one is true. \r\n\r\nalso, instruction in https://mixcr.readthedocs.io/en/master/assembleContigs.html state:\r\n# align raw sequences\r\nmixcr align --species mmu -p kAligner2 --report report.txt input_R1.fq input_R2.fq alignments.vdjca\r\nit should be  kaligner2 not  kAligner2\r\n\r\nfinally : \r\n# assemble default CDR3 clonotypes (note: --write-alignments is required for further contig assembly)\r\nmixcr assemble --write-alignments --report report.txt alignments.vdjca clones.clna\r\n\r\n# assemble full BCR receptors\r\nmixcr assembleContigs --report report.txt clones.clna full_clones.clns\r\n \r\nnone of these is working, any typo mistakes?\r\nthanks a lot\r\nibseq"},"comment":{"url":"https://api.github.com/repos/milaboratory/mixcr/issues/comments/448551688","html_url":"https://github.com/milaboratory/mixcr/issues/471#issuecomment-448551688","issue_url":"https://api.github.com/repos/milaboratory/mixcr/issues/471","id":448551688,"node_id":"MDEyOklzc3VlQ29tbWVudDQ0ODU1MTY4OA==","user":{"login":"dbolotin","id":3062854,"node_id":"MDQ6VXNlcjMwNjI4NTQ=","avatar_url":"https://avatars1.githubusercontent.com/u/3062854?v=4","gravatar_id":"","url":"https://api.github.com/users/dbolotin","html_url":"https://github.com/dbolotin","followers_url":"https://api.github.com/users/dbolotin/followers","following_url":"https://api.github.com/users/dbolotin/following{/other_user}","gists_url":"https://api.github.com/users/dbolotin/gists{/gist_id}","starred_url":"https://api.github.com/users/dbolotin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dbolotin/subscriptions","organizations_url":"https://api.github.com/users/dbolotin/orgs","repos_url":"https://api.github.com/users/dbolotin/repos","events_url":"https://api.github.com/users/dbolotin/events{/privacy}","received_events_url":"https://api.github.com/users/dbolotin/received_events","type":"User","site_admin":false},"created_at":"2018-12-19T10:48:50Z","updated_at":"2018-12-19T10:48:50Z","author_association":"MEMBER","body":"Hi, please create the folder before using it as a temporary storage. E.g.:\r\n```\r\nmkdir -p /home/ibassano/some_folder/\r\n```"}}
{"actor":{"display_login":"dbolotin"}}