{"action":"created","issue":{"url":"https://api.github.com/repos/taoliu/MACS/issues/74","labels_url":"https://api.github.com/repos/taoliu/MACS/issues/74/labels{/name}","comments_url":"https://api.github.com/repos/taoliu/MACS/issues/74/comments","events_url":"https://api.github.com/repos/taoliu/MACS/issues/74/events","html_url":"https://github.com/taoliu/MACS/issues/74","id":69163763,"number":74,"title":"Negative p-values when using --broad peak flag","user":{"login":"lopatica","id":11952613,"avatar_url":"https://avatars.githubusercontent.com/u/11952613?v=3","gravatar_id":"","url":"https://api.github.com/users/lopatica","html_url":"https://github.com/lopatica","followers_url":"https://api.github.com/users/lopatica/followers","following_url":"https://api.github.com/users/lopatica/following{/other_user}","gists_url":"https://api.github.com/users/lopatica/gists{/gist_id}","starred_url":"https://api.github.com/users/lopatica/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lopatica/subscriptions","organizations_url":"https://api.github.com/users/lopatica/orgs","repos_url":"https://api.github.com/users/lopatica/repos","events_url":"https://api.github.com/users/lopatica/events{/privacy}","received_events_url":"https://api.github.com/users/lopatica/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"taoliu","id":593654,"avatar_url":"https://avatars.githubusercontent.com/u/593654?v=3","gravatar_id":"","url":"https://api.github.com/users/taoliu","html_url":"https://github.com/taoliu","followers_url":"https://api.github.com/users/taoliu/followers","following_url":"https://api.github.com/users/taoliu/following{/other_user}","gists_url":"https://api.github.com/users/taoliu/gists{/gist_id}","starred_url":"https://api.github.com/users/taoliu/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/taoliu/subscriptions","organizations_url":"https://api.github.com/users/taoliu/orgs","repos_url":"https://api.github.com/users/taoliu/repos","events_url":"https://api.github.com/users/taoliu/events{/privacy}","received_events_url":"https://api.github.com/users/taoliu/received_events","type":"User","site_admin":false},"milestone":null,"comments":18,"created_at":"2015-04-17T15:43:23Z","updated_at":"2015-04-24T18:20:57Z","closed_at":null,"body":"I am using MACS2 to call open chromatin regions in a MNase-seq dataset. However I'm generating negative p-values after calling broad peaks using the following commands:\r\nmacs2 callpeak -t treatment.s.bam -c input.bam -n tg \\\r\n--outdir ~/nucleosomedata/ -f BAMPE -g 1.87e9 --broad\r\n\r\nHere is a few rows of output:\r\n\r\nchr\tstart\tend\tlength\tpileup\t-LOG10(pvalue)\tfold_enrichment\t-LOG10(qvalue)\tname\r\nchr1\t3003373\t3003936\t564\t-1.23335E+31\t-1.26269E+18\t1.36546E+30\t2.13806\ttg_peak_1\r\nchr1\t3020520\t3020966\t447\t-4.20326E+31\t-4.30325E+18\t4.65349E+30\t1.28417\ttg_peak_2\r\nchr1\t3029027\t3030664\t1638\t-1.39736E+31\t-1.4306E+18\t1.54704E+30\t1.49317\ttg_peak_3\r\nchr1\t3045122\t3045422\t301\t-5.30715E+31\t-5.4334E+18\t5.87561E+30\t1.26046\ttg_peak_4\r\n\r\nCould this be due to defaulting to q-values when calling broad peaks?\r\n\r\nThanks"},"comment":{"url":"https://api.github.com/repos/taoliu/MACS/issues/comments/96024016","html_url":"https://github.com/taoliu/MACS/issues/74#issuecomment-96024016","issue_url":"https://api.github.com/repos/taoliu/MACS/issues/74","id":96024016,"user":{"login":"lopatica2","id":12076570,"avatar_url":"https://avatars.githubusercontent.com/u/12076570?v=3","gravatar_id":"","url":"https://api.github.com/users/lopatica2","html_url":"https://github.com/lopatica2","followers_url":"https://api.github.com/users/lopatica2/followers","following_url":"https://api.github.com/users/lopatica2/following{/other_user}","gists_url":"https://api.github.com/users/lopatica2/gists{/gist_id}","starred_url":"https://api.github.com/users/lopatica2/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lopatica2/subscriptions","organizations_url":"https://api.github.com/users/lopatica2/orgs","repos_url":"https://api.github.com/users/lopatica2/repos","events_url":"https://api.github.com/users/lopatica2/events{/privacy}","received_events_url":"https://api.github.com/users/lopatica2/received_events","type":"User","site_admin":false},"created_at":"2015-04-24T18:20:57Z","updated_at":"2015-04-24T18:20:57Z","body":"Great to know! Thank you again.\n\nOn Fri, Apr 24, 2015 at 1:51 PM, Tao Liu (τν) <notifications@github.com>\nwrote:\n\n> @lopatica2 <https://github.com/lopatica2> As a general recommendation to\n> all people processing their own data on Linux/Unix and wondering how to\n> control bioinformatics tools by themselves, the 'virtualenv' tool will help\n> you. Google 'virtualenv' (https://virtualenv.pypa.io/en/latest/), there\n> is a simple python script you can use, to make a virtual python environment\n> isolated from the one for whole system and fully controlled by yourself. By\n> activating it, your current environmental variables will be changed so that\n> any software, not only python software, will be installed into this\n> isolated environment. No need to ask administrators anymore. So you will\n> have full control of installing, removing, updating tools. You may be able\n> to find some good tutorial on virtualenv on the web.\n>\n> —\n> Reply to this email directly or view it on GitHub\n> <https://github.com/taoliu/MACS/issues/74#issuecomment-96011981>.\n>\n\n\n\n-- \nGraham D Johnson\nGraduate Research Assistant\nCenter for Molecular Medicine and Genetics\nWayne State University School of Medicine\nDetroit MI 48201\nUSA\n\nPhone:         313-577-0765\nFAX:               313-577-8554\n"}}