{"action":"opened","issue":{"url":"https://api.github.com/repos/gpertea/stringtie/issues/192","repository_url":"https://api.github.com/repos/gpertea/stringtie","labels_url":"https://api.github.com/repos/gpertea/stringtie/issues/192/labels{/name}","comments_url":"https://api.github.com/repos/gpertea/stringtie/issues/192/comments","events_url":"https://api.github.com/repos/gpertea/stringtie/issues/192/events","html_url":"https://github.com/gpertea/stringtie/issues/192","id":349219443,"node_id":"MDU6SXNzdWUzNDkyMTk0NDM=","number":192,"title":"Issue of \"-e\" causing duplication in abundance estimation needs to be revisited","user":{"login":"JohnHadish","id":35115540,"node_id":"MDQ6VXNlcjM1MTE1NTQw","avatar_url":"https://avatars2.githubusercontent.com/u/35115540?v=4","gravatar_id":"","url":"https://api.github.com/users/JohnHadish","html_url":"https://github.com/JohnHadish","followers_url":"https://api.github.com/users/JohnHadish/followers","following_url":"https://api.github.com/users/JohnHadish/following{/other_user}","gists_url":"https://api.github.com/users/JohnHadish/gists{/gist_id}","starred_url":"https://api.github.com/users/JohnHadish/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/JohnHadish/subscriptions","organizations_url":"https://api.github.com/users/JohnHadish/orgs","repos_url":"https://api.github.com/users/JohnHadish/repos","events_url":"https://api.github.com/users/JohnHadish/events{/privacy}","received_events_url":"https://api.github.com/users/JohnHadish/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-08-09T17:25:08Z","updated_at":"2018-08-09T17:25:08Z","closed_at":null,"author_association":"NONE","body":"On the stringtie homepage [not github](https://ccb.jhu.edu/software/stringtie/index.shtml#install) , v1.3.1 supposedly fixed this issue: \r\n\r\n**\"fixed a duplication of some output transcripts in -e mode (abundance estimation only)\"**\r\n\r\nI am currently running stringtie on Arabidopsis rna-seq data sets and I am encountering duplication events that vary from sample to sample. The command I am running is:\r\n```\r\nstringtie -v -p 1 -e -o test.gtf -G TAIR10_Araport11.gtf -A test.ga -l test OutputFromHisat-Samtools_sort-Samtoools_Index.bam\r\n\r\n```\r\nI am using the arabidopsis gtf downloaded from TAIR, and the reads I am running are downloaded from NCBI. My workflow is trimmomatic, hisat2, samtools_sort, samtools_index, stringtie. I am running  stringtie v1.3.4d. My workflow was run on a llinux slurm cluster, and I have also verified the same results on my local machine (Ubuntu 18.04).\r\n\r\nI typically have 1 or 2 genes per run that have duplication events.\r\n\r\nA colleague running the same workflow on bovine data is having the same issue. \r\n\r\nAny help would be greatly appreciated.\r\nThank you for your time! "}}
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