{"action":"created","issue":{"url":"https://api.github.com/repos/djhn75/RNAEditor/issues/16","repository_url":"https://api.github.com/repos/djhn75/RNAEditor","labels_url":"https://api.github.com/repos/djhn75/RNAEditor/issues/16/labels{/name}","comments_url":"https://api.github.com/repos/djhn75/RNAEditor/issues/16/comments","events_url":"https://api.github.com/repos/djhn75/RNAEditor/issues/16/events","html_url":"https://github.com/djhn75/RNAEditor/issues/16","id":295136053,"number":16,"title":"Remove Duplicates","user":{"login":"WYSNI","id":27208245,"avatar_url":"https://avatars3.githubusercontent.com/u/27208245?v=4","gravatar_id":"","url":"https://api.github.com/users/WYSNI","html_url":"https://github.com/WYSNI","followers_url":"https://api.github.com/users/WYSNI/followers","following_url":"https://api.github.com/users/WYSNI/following{/other_user}","gists_url":"https://api.github.com/users/WYSNI/gists{/gist_id}","starred_url":"https://api.github.com/users/WYSNI/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/WYSNI/subscriptions","organizations_url":"https://api.github.com/users/WYSNI/orgs","repos_url":"https://api.github.com/users/WYSNI/repos","events_url":"https://api.github.com/users/WYSNI/events{/privacy}","received_events_url":"https://api.github.com/users/WYSNI/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-02-07T13:24:05Z","updated_at":"2018-02-08T09:48:05Z","closed_at":null,"author_association":"NONE","body":"Hi David, \r\n\r\nI have a question about the \"Remove PCR duplicates\" step:\r\n\r\nIn your code, (see below) i think you just mark duplicates reads or not remove them because you just use the picard tool MarkDuplicates. The step rmdup is in comment .\r\n\r\nI'm wrong?\r\n\r\n#mark PCR duplicates\r\n        #Helper.status(\"Remove Duplicates\", self.rnaEdit.logFile,self.rnaEdit.textField)\r\n        markedFile=self.rnaEdit.params.output+\".noDup.bam\"\r\n        cmd=[\"java\",\"-Xmx16G\",\"-jar\",self.rnaEdit.params.sourceDir + \"picard-tools/MarkDuplicates.jar\",\"INPUT=\" + bamFile, \"OUTPUT=\" + markedFile, \"METRICS_FILE=\"+self.rnaEdit.params.output+\".pcr.metrics\", \"VALIDATION_STRINGENCY=LENIENT\", \"CREATE_INDEX=true\"]\r\n        Helper.proceedCommand(\"Remove PCR duplicates\", cmd, bamFile, markedFile, self.rnaEdit)\r\n        \r\n        \r\n        \"\"\"if self.rnaEdit.params.paired == False:\r\n            pysam.rmdup(\"-s\",bamFile,markedFile)\r\n        else:\r\n            pysam.rmdup(bamFile,markedFile)\r\n        #pysam.rmdup(bamFile,markedFile)\r\n        if self.rnaEdit.params.paired == False:\r\n            cmd = [self.rnaEdit.params.sourceDir + \"samtools\", \"rmdup\", \"-s\", bamFile, markedFile]\r\n        else:\r\n            cmd = [self.rnaEdit.params.sourceDir + \"samtools\", \"rmdup\", bamFile, markedFile]\r\n        Helper.proceedCommand(\"Index Bam File\", cmd, bamFile, markedFile, self.rnaEdit)\r\n        \r\n        \r\n        Helper.status(\"index Bam\", self.rnaEdit.logFile,self.rnaEdit.textField)\r\n        pysam.index(markedFile)\r\n        \r\n        cmd = [self.rnaEdit.params.sourceDir + \"samtools\", \"index\", bamFile]\r\n        Helper.proceedCommand(\"Index Bam File\", cmd, bamFile, markedFile+\".bai\", self.rnaEdit)\r\n        #return bamFile\"\"\"\r\n\r\n\r\nWhere did you remove duplicates reads?\r\n\r\nBest,\r\n\r\nWYSNI"},"comment":{"url":"https://api.github.com/repos/djhn75/RNAEditor/issues/comments/364057840","html_url":"https://github.com/djhn75/RNAEditor/issues/16#issuecomment-364057840","issue_url":"https://api.github.com/repos/djhn75/RNAEditor/issues/16","id":364057840,"user":{"login":"djhn75","id":5654514,"avatar_url":"https://avatars1.githubusercontent.com/u/5654514?v=4","gravatar_id":"","url":"https://api.github.com/users/djhn75","html_url":"https://github.com/djhn75","followers_url":"https://api.github.com/users/djhn75/followers","following_url":"https://api.github.com/users/djhn75/following{/other_user}","gists_url":"https://api.github.com/users/djhn75/gists{/gist_id}","starred_url":"https://api.github.com/users/djhn75/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/djhn75/subscriptions","organizations_url":"https://api.github.com/users/djhn75/orgs","repos_url":"https://api.github.com/users/djhn75/repos","events_url":"https://api.github.com/users/djhn75/events{/privacy}","received_events_url":"https://api.github.com/users/djhn75/received_events","type":"User","site_admin":false},"created_at":"2018-02-08T09:48:05Z","updated_at":"2018-02-08T09:48:05Z","author_association":"OWNER","body":"Dear WYSNI, you are totally right, the duplicates are simply marked, yet afterward those marked reads are ignored by GATK. \nTherefore duplicate reads cannot influence the SNP ratio.\n\nWe tested samtools rmdup too, therefore it is still in the code, but we recognised that GATK often crashes after we used samtools, because of incorrect formed files.\n\nThanks for your interest in RNAEditor\n\nBest regards David\nDavid John\nInstitute of Cardiovascular Regeneration\nTheodor-Stern-Kai 7\nD-60590 Frankfurt am Main\n+49 69 6301 87952\nJohn@med.uni-frankfurt.de <mailto:John@med.uni-frankfurt.de>\n\n\n\n> Am 07.02.2018 um 14:24 schrieb WYSNI <notifications@github.com <mailto:notifications@github.com>>:\n> \n> Hi David,\n> \n> I have a question about the \"Remove PCR duplicates\" step:\n> \n> In your code, (see below) i think you just mark duplicates reads or not remove them because you just use the picard tool MarkDuplicates. The step rmdup is in comment .\n> \n> I'm wrong?\n> \n> #mark PCR duplicates\n> #Helper.status(\"Remove Duplicates\", self.rnaEdit.logFile,self.rnaEdit.textField)\n> markedFile=self.rnaEdit.params.output+\".noDup.bam\"\n> cmd=[\"java\",\"-Xmx16G\",\"-jar\",self.rnaEdit.params.sourceDir + \"picard-tools/MarkDuplicates.jar\",\"INPUT=\" + bamFile, \"OUTPUT=\" + markedFile, \"METRICS_FILE=\"+self.rnaEdit.params.output+\".pcr.metrics\", \"VALIDATION_STRINGENCY=LENIENT\", \"CREATE_INDEX=true\"]\n> Helper.proceedCommand(\"Remove PCR duplicates\", cmd, bamFile, markedFile, self.rnaEdit)\n> \n>     \"\"\"if self.rnaEdit.params.paired == False:\n>         pysam.rmdup(\"-s\",bamFile,markedFile)\n>     else:\n>         pysam.rmdup(bamFile,markedFile)\n>     #pysam.rmdup(bamFile,markedFile)\n>     if self.rnaEdit.params.paired == False:\n>         cmd = [self.rnaEdit.params.sourceDir + \"samtools\", \"rmdup\", \"-s\", bamFile, markedFile]\n>     else:\n>         cmd = [self.rnaEdit.params.sourceDir + \"samtools\", \"rmdup\", bamFile, markedFile]\n>     Helper.proceedCommand(\"Index Bam File\", cmd, bamFile, markedFile, self.rnaEdit)\n>     \n>     \n>     Helper.status(\"index Bam\", self.rnaEdit.logFile,self.rnaEdit.textField)\n>     pysam.index(markedFile)\n>     \n>     cmd = [self.rnaEdit.params.sourceDir + \"samtools\", \"index\", bamFile]\n>     Helper.proceedCommand(\"Index Bam File\", cmd, bamFile, markedFile+\".bai\", self.rnaEdit)\n>     #return bamFile\"\"\"\n> Where did you remove duplicates reads?\n> \n> Best,\n> \n> WYSNI\n> \n> —\n> You are receiving this because you are subscribed to this thread.\n> Reply to this email directly, view it on GitHub <https://github.com/djhn75/RNAEditor/issues/16>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AFZH8twZ9u2rnNxPfoUPc1za7CJAXaZkks5tSaP1gaJpZM4R8s8s>.\n> \n> {\"api_version\":\"1.0\",\"publisher\":{\"api_key\":\"05dde50f1d1a384dd78767c55493e4bb\",\"name\":\"GitHub\"},\"entity\":{\"external_key\":\"github/djhn75/RNAEditor\",\"title\":\"djhn75/RNAEditor\",\"subtitle\":\"GitHub repository\",\"main_image_url\":\"https://cloud.githubusercontent.com/assets/143418/17495839/a5054eac-5d88-11e6-95fc-7290892c7bb5.png <https://cloud.githubusercontent.com/assets/143418/17495839/a5054eac-5d88-11e6-95fc-7290892c7bb5.png>\",\"avatar_image_url\":\"https://cloud.githubusercontent.com/assets/143418/15842166/7c72db34-2c0b-11e6-9aed-b52498112777.png <https://cloud.githubusercontent.com/assets/143418/15842166/7c72db34-2c0b-11e6-9aed-b52498112777.png>\",\"action\":{\"name\":\"Open in GitHub\",\"url\":\"https://github.com/djhn75/RNAEditor <https://github.com/djhn75/RNAEditor>\"}},\"updates\":{\"snippets\":[{\"icon\":\"DESCRIPTION\",\"message\":\"Remove Duplicates (#16)\"}],\"action\":{\"name\":\"View Issue\",\"url\":\"https://github.com/djhn75/RNAEditor/issues/16 <https://github.com/djhn75/RNAEditor/issues/16>\"}}}\n\n"}}
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