{"action":"created","issue":{"url":"https://api.github.com/repos/itmat/Normalization/issues/33","labels_url":"https://api.github.com/repos/itmat/Normalization/issues/33/labels{/name}","comments_url":"https://api.github.com/repos/itmat/Normalization/issues/33/comments","events_url":"https://api.github.com/repos/itmat/Normalization/issues/33/events","html_url":"https://github.com/itmat/Normalization/issues/33","id":64336696,"number":33,"title":"depth for intron and exon quantication","user":{"login":"e-manduchi","id":2163635,"avatar_url":"https://avatars.githubusercontent.com/u/2163635?v=3","gravatar_id":"","url":"https://api.github.com/users/e-manduchi","html_url":"https://github.com/e-manduchi","followers_url":"https://api.github.com/users/e-manduchi/followers","following_url":"https://api.github.com/users/e-manduchi/following{/other_user}","gists_url":"https://api.github.com/users/e-manduchi/gists{/gist_id}","starred_url":"https://api.github.com/users/e-manduchi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/e-manduchi/subscriptions","organizations_url":"https://api.github.com/users/e-manduchi/orgs","repos_url":"https://api.github.com/users/e-manduchi/repos","events_url":"https://api.github.com/users/e-manduchi/events{/privacy}","received_events_url":"https://api.github.com/users/e-manduchi/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2015-03-25T18:09:53Z","updated_at":"2015-03-25T21:06:27Z","closed_at":null,"body":"Hello, I've issues the command with the option -depthExon 5 and -depthIntron 5\r\nHowever the first call to quantification of exon and introns appears to continue using the default:\r\n\r\nQ.SAMPLE.quantify_exons_introns_u.sh\r\n\r\nhas -depthE 20 -depthI 10 specified."},"comment":{"url":"https://api.github.com/repos/itmat/Normalization/issues/comments/86217960","html_url":"https://github.com/itmat/Normalization/issues/33#issuecomment-86217960","issue_url":"https://api.github.com/repos/itmat/Normalization/issues/33","id":86217960,"user":{"login":"e-manduchi","id":2163635,"avatar_url":"https://avatars.githubusercontent.com/u/2163635?v=3","gravatar_id":"","url":"https://api.github.com/users/e-manduchi","html_url":"https://github.com/e-manduchi","followers_url":"https://api.github.com/users/e-manduchi/followers","following_url":"https://api.github.com/users/e-manduchi/following{/other_user}","gists_url":"https://api.github.com/users/e-manduchi/gists{/gist_id}","starred_url":"https://api.github.com/users/e-manduchi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/e-manduchi/subscriptions","organizations_url":"https://api.github.com/users/e-manduchi/orgs","repos_url":"https://api.github.com/users/e-manduchi/repos","events_url":"https://api.github.com/users/e-manduchi/events{/privacy}","received_events_url":"https://api.github.com/users/e-manduchi/received_events","type":"User","site_admin":false},"created_at":"2015-03-25T21:06:27Z","updated_at":"2015-03-25T21:06:27Z","body":"Thanks for the clarification. Oddly though, I discovered this after I got the script to exit before completing. When I manually modified my copy of quantify_exons_introns to use 5 as default depth and I resumed the pipeline, it went through with no error. Maybe it was a coincidence."}}