{"action":"closed","issue":{"url":"https://api.github.com/repos/davidaknowles/leafcutter/issues/84","repository_url":"https://api.github.com/repos/davidaknowles/leafcutter","labels_url":"https://api.github.com/repos/davidaknowles/leafcutter/issues/84/labels{/name}","comments_url":"https://api.github.com/repos/davidaknowles/leafcutter/issues/84/comments","events_url":"https://api.github.com/repos/davidaknowles/leafcutter/issues/84/events","html_url":"https://github.com/davidaknowles/leafcutter/issues/84","id":376790639,"node_id":"MDU6SXNzdWUzNzY3OTA2Mzk=","number":84,"title":"Extract split reads supporting a cluster","user":{"login":"dfermin","id":3055867,"node_id":"MDQ6VXNlcjMwNTU4Njc=","avatar_url":"https://avatars3.githubusercontent.com/u/3055867?v=4","gravatar_id":"","url":"https://api.github.com/users/dfermin","html_url":"https://github.com/dfermin","followers_url":"https://api.github.com/users/dfermin/followers","following_url":"https://api.github.com/users/dfermin/following{/other_user}","gists_url":"https://api.github.com/users/dfermin/gists{/gist_id}","starred_url":"https://api.github.com/users/dfermin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dfermin/subscriptions","organizations_url":"https://api.github.com/users/dfermin/orgs","repos_url":"https://api.github.com/users/dfermin/repos","events_url":"https://api.github.com/users/dfermin/events{/privacy}","received_events_url":"https://api.github.com/users/dfermin/received_events","type":"User","site_admin":false},"labels":[{"id":285450413,"node_id":"MDU6TGFiZWwyODU0NTA0MTM=","url":"https://api.github.com/repos/davidaknowles/leafcutter/labels/help%20wanted","name":"help wanted","color":"159818","default":true}],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2018-11-02T12:29:04Z","updated_at":"2018-12-10T17:41:02Z","closed_at":"2018-12-10T17:41:02Z","author_association":"NONE","body":"Hi\r\nI'm trying to extract the reads that leafcutter uses in it's output `*_perind.counts.gz`. For instance I see this line in my data:\r\n```\r\nchrom samp1 samp2\r\n14:20764605:20766956:clu_5_NA   147/336 203/411\r\n```\r\nThis says that the first and second samples had 147 and 203 reads respectively supporting the cluster in my data set. \r\n\r\nBut when I run samtools on these BAM files I can't get out those reads. \r\nI'm using `samtools view -f 256 samp1.bam 14:20764605-20766956` as the command to extract the reads. Perhaps this is the wrong command.\r\n\r\nCould you advice on how to identify the reads of interest used by leafcutter?\r\nIn case it helps: my data is human paired-end RNAseq data aligned to GRCh37 using STAR 2.6.\r\n\r\nThanks in advance for any and all help."}}
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