{"action":"created","issue":{"url":"https://api.github.com/repos/TreesLab/NCLscan/issues/5","repository_url":"https://api.github.com/repos/TreesLab/NCLscan","labels_url":"https://api.github.com/repos/TreesLab/NCLscan/issues/5/labels{/name}","comments_url":"https://api.github.com/repos/TreesLab/NCLscan/issues/5/comments","events_url":"https://api.github.com/repos/TreesLab/NCLscan/issues/5/events","html_url":"https://github.com/TreesLab/NCLscan/issues/5","id":139871212,"number":5,"title":"Where are Total number of all support reads, Total number of junc-reads, Total number of span-reads in .result file","user":{"login":"NitinMandloi","id":17763582,"avatar_url":"https://avatars.githubusercontent.com/u/17763582?v=3","gravatar_id":"","url":"https://api.github.com/users/NitinMandloi","html_url":"https://github.com/NitinMandloi","followers_url":"https://api.github.com/users/NitinMandloi/followers","following_url":"https://api.github.com/users/NitinMandloi/following{/other_user}","gists_url":"https://api.github.com/users/NitinMandloi/gists{/gist_id}","starred_url":"https://api.github.com/users/NitinMandloi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/NitinMandloi/subscriptions","organizations_url":"https://api.github.com/users/NitinMandloi/orgs","repos_url":"https://api.github.com/users/NitinMandloi/repos","events_url":"https://api.github.com/users/NitinMandloi/events{/privacy}","received_events_url":"https://api.github.com/users/NitinMandloi/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":5,"created_at":"2016-03-10T12:21:25Z","updated_at":"2016-03-11T07:00:36Z","closed_at":null,"body":"Hi\r\n\r\n   I am using NCLscan for my RNA seq data. I am able to run the full pipeline. I got my sam and tab delimited result file. I am unable to see Total number of all support reads, Total number of junc-reads, Total number of span-reads in .result file.\r\n\r\nAlso if I want to import the sam file to IGV to just validate the results. Can I use result.sam file to IGV? \r\n\r\nKindly help me regarding the same.\r\n\r\nThank you\r\n\r\nRegards"},"comment":{"url":"https://api.github.com/repos/TreesLab/NCLscan/issues/comments/195226314","html_url":"https://github.com/TreesLab/NCLscan/issues/5#issuecomment-195226314","issue_url":"https://api.github.com/repos/TreesLab/NCLscan/issues/5","id":195226314,"user":{"login":"chiangtw","id":7620618,"avatar_url":"https://avatars.githubusercontent.com/u/7620618?v=3","gravatar_id":"","url":"https://api.github.com/users/chiangtw","html_url":"https://github.com/chiangtw","followers_url":"https://api.github.com/users/chiangtw/followers","following_url":"https://api.github.com/users/chiangtw/following{/other_user}","gists_url":"https://api.github.com/users/chiangtw/gists{/gist_id}","starred_url":"https://api.github.com/users/chiangtw/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/chiangtw/subscriptions","organizations_url":"https://api.github.com/users/chiangtw/orgs","repos_url":"https://api.github.com/users/chiangtw/repos","events_url":"https://api.github.com/users/chiangtw/events{/privacy}","received_events_url":"https://api.github.com/users/chiangtw/received_events","type":"User","site_admin":false},"created_at":"2016-03-11T07:00:36Z","updated_at":"2016-03-11T07:00:36Z","body":"You may just copy two new scripts \"Add_read_count.py\" and \"utils.py\" into your project directory, and run the following command:\r\n\r\n    > ./Add_read_count.py -pj [Project_name] -tmp [Your_original_result_file] -sam [The_result_sam_file] -o [Output_file_name]\r\n\r\nAnd the last three columns of the output would be the total numbers of support/junc/span reads.\r\n\r\nThanks."}}