{"action":"opened","issue":{"url":"https://api.github.com/repos/Xinglab/lr2rmats/issues/4","repository_url":"https://api.github.com/repos/Xinglab/lr2rmats","labels_url":"https://api.github.com/repos/Xinglab/lr2rmats/issues/4/labels{/name}","comments_url":"https://api.github.com/repos/Xinglab/lr2rmats/issues/4/comments","events_url":"https://api.github.com/repos/Xinglab/lr2rmats/issues/4/events","html_url":"https://github.com/Xinglab/lr2rmats/issues/4","id":365141662,"node_id":"MDU6SXNzdWUzNjUxNDE2NjI=","number":4,"title":"l2rmats really doesn't like comparing opposite strands","user":{"login":"leipzig","id":147991,"node_id":"MDQ6VXNlcjE0Nzk5MQ==","avatar_url":"https://avatars3.githubusercontent.com/u/147991?v=4","gravatar_id":"","url":"https://api.github.com/users/leipzig","html_url":"https://github.com/leipzig","followers_url":"https://api.github.com/users/leipzig/followers","following_url":"https://api.github.com/users/leipzig/following{/other_user}","gists_url":"https://api.github.com/users/leipzig/gists{/gist_id}","starred_url":"https://api.github.com/users/leipzig/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/leipzig/subscriptions","organizations_url":"https://api.github.com/users/leipzig/orgs","repos_url":"https://api.github.com/users/leipzig/repos","events_url":"https://api.github.com/users/leipzig/events{/privacy}","received_events_url":"https://api.github.com/users/leipzig/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-09-29T15:28:55Z","updated_at":"2018-09-29T15:28:55Z","closed_at":null,"author_association":"NONE","body":"Hi - virtually any opposite strand query.sam vs rRNA.gtf alignments seem to trigger a `[trans_exon_comp] Strands of exons do NOT match.` error. Should I be converting all the rRNA strands to `.`?\r\n\r\nhere's a reproducible example:\r\n\r\nrRNA.gtf\r\n```\r\nchr1\thg38_rmsk\texon\t629499\t629570\t429.000000\t-\t.\tgene_id \"tRNA-Gln-CAA_\"; transcript_id \"tRNA-Gln-CAA_\"; \r\nchr1\thg38_rmsk\texon\t632619\t632685\t432.000000\t-\t.\tgene_id \"tRNA-Ser-TCA(m)\"; transcript_id \"tRNA-Ser-TCA(m)\"; \r\nchr1\thg38_rmsk\texon\t1883669\t1883765\t515.000000\t+\t.\tgene_id \"LSU-rRNA_Hsa\"; transcript_id \"LSU-rRNA_Hsa\"; \r\n```\r\n\r\nsamp1.minimap.sam\r\n```\r\n@SQ\tSN:chr1\tLN:1153837\r\n@PG\tID:minimap2\tPN:minimap2\tVN:2.12-r827\tCL:minimap2 -ax splice -ub -t 1 test_data/genome/genome.fa.smmi test_data/read/SRR5009429.fasta\r\nSRR5009429.9366 0       chr1    134065  1       24S1M1D49M1D16M115855N1I34M1D9M1D70M1D109M1I14M1001S    *       0       0       AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGATGAAGGCTTGCTCTGTCTCCAGGCTGGAGTGCAATGGCACGATCTCAGCTCACTGCAACGTCCACCTCCGGGTTCAAGCATTCTTCTGCCTCAGCCTCCAGAGTAGCTGGGATTACAGGCGCCTGCCACCACACCCAGCTAATTTTTCTATTTTTAGTAGAGACAGGGTTTCACCATCTTGGTCAGGCTGGTCTCAAACTCCTGACCTCAGGTGATCCACCCGCCTCAGCCTCCCAAAGTGCTGGGATTACAGGCGTTGAGCTACCGCGCCCGGATCCGTAAGTGATCTTACATCAACTAGAACATACTTAAGAGTGAAAAATTATACAATGGTTTCTTCCCTCTCCTGTAGAAATGTTACCATAATTAAATGTTTGATCAATTGCTAAATCACAACTTACAATATGAAAATCTTCATATACTTCAAATATACTGAAGAAAATGTCCTACATGTAACTGAGGTGCGCATCCACCTGAATGAACAGCACGAAACGCTATTAAAGTGACACTAGAAGCCCAGGCACAAATCATACACAGACACAAAAAAGCTCCAGATCCCACTCAGGAAGAATGCACCAACACATTCGCATTTATTTTCTTTTTTTTTTTTAAAGCAAATGACAAAGACCCAGTTTACCAGCTTTACTTTTTTAAACCTAAGCTTAACATTACATATTTAAACAATTGTCAAACTTACTAAGTTGCCAGCATTCATGCACAACTAGAAAACATCCTTAATTTATATTAACCAGAAATGTATTACCATTAATGTATTAATATCTTTCACTACTAAATACTGAAAAAATTGAAATTATTTCTGTAGAAGAATCGTCCTGGCAATGTTAACTTCACAGCAGGCCGACACTACGTGGCTCACATTTCAGACACAATGAAAAGCAGGTCCATGCTGGTGTTAGTGTACAATCTTGTCCTACACTAAAGAGTCAAGACTCACCTTGAGTACGTTTAATAAAAAGCAAAGTGCATACAGAGATTTACAACAATTTTAAAGACAAAAAAAATGGTCCTATTATGTGGTCCAACAATCAACTCAAAAGTCTATGACAAATAGAGGCTCCGATGAGCTGTTTATAAATACTTTAGGTACAATTATACTGAAAGTCGAGTTCGTTTGAAATCTTCAAAAAAATGTTCCTGTTAATCCTCAAATGGTGCTTGTTATAGTTTAACATTTCTGTTAAGTGCGTGCGTTTGAATTACTTGTTATCCAAGCGCAGCAGCTGCTCCTTACTCTGCGTTGATACCACTGCT *       NM:i:36 ms:i:196        AS:i:162        nn:i:0  ts:A:+  tp:A:P  cm:i:14 s1:i:82 s2:i:106        dv:f:0.1136     SA:Z:chr1,1069470,-,662S643M55396D24S,24,367;\r\n```\r\n\r\nlr2rmats filter samp1.minimap.sam -r rRNA.gtf -v 0.67 -q 0.75 -s 0.98\r\n[trans_exon_comp] Strands of exons do NOT match.\r\n\r\nthanks for your help and awesome C code!"}}
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