{"action":"created","issue":{"url":"https://api.github.com/repos/alexdobin/STAR/issues/495","repository_url":"https://api.github.com/repos/alexdobin/STAR","labels_url":"https://api.github.com/repos/alexdobin/STAR/issues/495/labels{/name}","comments_url":"https://api.github.com/repos/alexdobin/STAR/issues/495/comments","events_url":"https://api.github.com/repos/alexdobin/STAR/issues/495/events","html_url":"https://github.com/alexdobin/STAR/issues/495","id":363582472,"node_id":"MDU6SXNzdWUzNjM1ODI0NzI=","number":495,"title":"[bug] Silent error causes false negative chimeric read","user":{"login":"jaudoux","id":3246711,"node_id":"MDQ6VXNlcjMyNDY3MTE=","avatar_url":"https://avatars3.githubusercontent.com/u/3246711?v=4","gravatar_id":"","url":"https://api.github.com/users/jaudoux","html_url":"https://github.com/jaudoux","followers_url":"https://api.github.com/users/jaudoux/followers","following_url":"https://api.github.com/users/jaudoux/following{/other_user}","gists_url":"https://api.github.com/users/jaudoux/gists{/gist_id}","starred_url":"https://api.github.com/users/jaudoux/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jaudoux/subscriptions","organizations_url":"https://api.github.com/users/jaudoux/orgs","repos_url":"https://api.github.com/users/jaudoux/repos","events_url":"https://api.github.com/users/jaudoux/events{/privacy}","received_events_url":"https://api.github.com/users/jaudoux/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-09-25T13:36:28Z","updated_at":"2018-09-25T14:03:19Z","closed_at":null,"author_association":"NONE","body":"Dear @alexdobin ,\r\n\r\nI have recently been using STAR to detect chimeric RNA in contigs for the DEkupl projet (https://github.com/Transipedia/dekupl-run).\r\n\r\nI faced a problem with my toy test file where I introduced a synthetic chimeric RNA that was not detected by STAR. My command for running STAR (v2.6.1b) is the following : \r\n\r\n```\r\nSTAR --runThreadN 1 --genomeDir test_index//star --readFilesIn bug.fastq.tmp --outFileNamePrefix test_STAR/ --twopassMode None --outSAMtype None --outReadsUnmapped None --al\r\nignIntronMax 100000 --chimSegmentMin 12 --chimJunctionOverhangMin 12 --alignSJDBoverhangMin 10 --chimSegmentReadGapMax 3 --alignSJstitchMismatchNmax 5 -1 5 5\r\n```\r\n\r\nFirst, I tried this FASTA file with a synthetic chimeric RNA : \r\n\r\n```\r\n>fusion\r\nGGAGCATCTCACAGATACGTTTATTCATACCACAAAGTAAACACTATTCAGGTATGTAGTGATGTTCCACGTTCCTGTGGTTGTAGGAGGAGGCCTTTCGGATAGCACCCCCTAGTTCTGCCCCTCATATCTGCTTCCTTGGTCTCTCCTGATTACTTGCTGTTTCTTTTCTTTTTTT\r\n```\r\n\r\nThe Chimeric.out.junction does record my chimeric RNA (chRNA)\r\n\r\n```\r\n22      41282761        -       22      41282940        -       1       0       1       fusion   41282762        102S76M 41282838        102M76S\r\n```\r\n\r\nHowever When the fusion is placed after this particular contig, it seems that a silent error occurs, and the chRNA is not found. Aside from the size of the contig (862nt), nothing looks strange in the input data.\r\n\r\n```\r\n>long-contig\r\nGGCGTCCCTTCCCCAATTTCCACAGAGACGTGCTCACCGGCTACATATGTCATGATTCTATGTCCAACCACAGGCCCAACCCTCAGGACAGACCCCGCCACCCCCCTTCTCTGCAGCTCCTGGCAGGGACGGTGCACAGTGGTGCCGTGTGCAGGGGGCCAGCGCAGCCACTGGGCATCTGGGGCAGCGCTGGTCGCCTGGCCACCTCCTTGCTGGGGCCGCTGGGCCTCCGGCCTAGAAGGACAGGAAGCCATCCACCTCAAGGCGCAGGAAGGGGTCCAGCAGGGCCCGGAGCTTCCAGATGGTGGCACGGCTCAGCAGGGGCGGCACCAGCCCCTCGAAGGGCCTGGGGTTCACCATGTACACGTAGGCGACCAGCAGGGTGCCCAGCAGCAGCCTCAGGATCAGCAGCCTACGGGCGGTGGCAGTCAGGGCCAGGGGCACGCAGGGGGCCTGGGGGCTGGGCTCTGCCACACAGTCACCTACCAGAGCTGGCCTGCCAGGCCCTTGGAGCTTTCCAACTTTGGTCTCCCTTTCTGATGGGGAGGGGAGCCCACTCCGAGGGTCCAGGCTGAGGGCGGGGATCCCTGGCTTTGGGAAACCCTCCTCAGACAGGGCTCCCCGCACCGCAGCCCTGGCCCCTTCCTCCTGGACAGGCTCCTGCAGCCACTTTTCAGATGCCCCCCACCCTGGACCTGCTCTGCTGGAGCTCATTTCTCCCCCTTGCCCAAGCAGGGTGCTGGGTGGGGGGCTGGTCTCCAGACCCAGAGTGGGGCGTGGGGGGCTCACTGCCATGCTCGCCATCTGCGGCTCCTTCTTGGCCTGAGTGTGGCACTGGGCCCGCTCCCTGCAGAGGCCTCAC\r\n>fusion\r\nGGAGCATCTCACAGATACGTTTATTCATACCACAAAGTAAACACTATTCAGGTATGTAGTGATGTTCCACGTTCCTGTGGTTGTAGGAGGAGGCCTTTCGGATAGCACCCCCTAGTTCTGCCCCTCATATCTGCTTCCTTGGTCTCTCCTGATTACTTGCTGTTTCTTTTCTTTTTTT\r\n```\r\n\r\nDo you have a idea of what is happening ?\r\n\r\nBest,\r\nJérôme."},"comment":{"url":"https://api.github.com/repos/alexdobin/STAR/issues/comments/424356078","html_url":"https://github.com/alexdobin/STAR/issues/495#issuecomment-424356078","issue_url":"https://api.github.com/repos/alexdobin/STAR/issues/495","id":424356078,"node_id":"MDEyOklzc3VlQ29tbWVudDQyNDM1NjA3OA==","user":{"login":"jaudoux","id":3246711,"node_id":"MDQ6VXNlcjMyNDY3MTE=","avatar_url":"https://avatars3.githubusercontent.com/u/3246711?v=4","gravatar_id":"","url":"https://api.github.com/users/jaudoux","html_url":"https://github.com/jaudoux","followers_url":"https://api.github.com/users/jaudoux/followers","following_url":"https://api.github.com/users/jaudoux/following{/other_user}","gists_url":"https://api.github.com/users/jaudoux/gists{/gist_id}","starred_url":"https://api.github.com/users/jaudoux/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jaudoux/subscriptions","organizations_url":"https://api.github.com/users/jaudoux/orgs","repos_url":"https://api.github.com/users/jaudoux/repos","events_url":"https://api.github.com/users/jaudoux/events{/privacy}","received_events_url":"https://api.github.com/users/jaudoux/received_events","type":"User","site_admin":false},"created_at":"2018-09-25T14:03:19Z","updated_at":"2018-09-25T14:03:19Z","author_association":"NONE","body":"@alexdobin I think it definitly comes from the contig size. I replaced the long contig with another one and the chRNA is not detected. But when I shorten the read to 650nt it does work!"}}
{"actor":{"display_login":"jaudoux"}}