{"action":"created","issue":{"url":"https://api.github.com/repos/lidaof/methylQA/issues/1","labels_url":"https://api.github.com/repos/lidaof/methylQA/issues/1/labels{/name}","comments_url":"https://api.github.com/repos/lidaof/methylQA/issues/1/comments","events_url":"https://api.github.com/repos/lidaof/methylQA/issues/1/events","html_url":"https://github.com/lidaof/methylQA/issues/1","id":107199541,"number":1,"title":"CpG file for bismark mode","user":{"login":"avilella","id":158007,"avatar_url":"https://avatars.githubusercontent.com/u/158007?v=3","gravatar_id":"","url":"https://api.github.com/users/avilella","html_url":"https://github.com/avilella","followers_url":"https://api.github.com/users/avilella/followers","following_url":"https://api.github.com/users/avilella/following{/other_user}","gists_url":"https://api.github.com/users/avilella/gists{/gist_id}","starred_url":"https://api.github.com/users/avilella/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/avilella/subscriptions","organizations_url":"https://api.github.com/users/avilella/orgs","repos_url":"https://api.github.com/users/avilella/repos","events_url":"https://api.github.com/users/avilella/events{/privacy}","received_events_url":"https://api.github.com/users/avilella/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":4,"created_at":"2015-09-18T13:10:50Z","updated_at":"2015-09-18T15:08:11Z","closed_at":null,"body":"I am trying to use methylQA bismark mode. I am mostly interested in the .report file that comes out of it. I wonder if you could guide me in how to produce the input files needed for it:\r\n\r\n- bam files: I got paired-end bam files from bismark 0.14.4\r\n- genome size file. I produced a file with this command:\r\n\r\nmysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -N -e         \"select chrom, size from hg38.chromInfo\" | head -n 24 > hg38.genome\r\n\r\n- CpG bed file:\r\n/path/of/CpG_no_contig.bed\r\n\r\nCan you tell me how I can manage to produce this file for human hg38? Am I right in thinking that this file with have approximately 28,000,000 entries?\r\n\r\nThanks,\r\n"},"comment":{"url":"https://api.github.com/repos/lidaof/methylQA/issues/comments/141478411","html_url":"https://github.com/lidaof/methylQA/issues/1#issuecomment-141478411","issue_url":"https://api.github.com/repos/lidaof/methylQA/issues/1","id":141478411,"user":{"login":"lidaof","id":102806,"avatar_url":"https://avatars.githubusercontent.com/u/102806?v=3","gravatar_id":"","url":"https://api.github.com/users/lidaof","html_url":"https://github.com/lidaof","followers_url":"https://api.github.com/users/lidaof/followers","following_url":"https://api.github.com/users/lidaof/following{/other_user}","gists_url":"https://api.github.com/users/lidaof/gists{/gist_id}","starred_url":"https://api.github.com/users/lidaof/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lidaof/subscriptions","organizations_url":"https://api.github.com/users/lidaof/orgs","repos_url":"https://api.github.com/users/lidaof/repos","events_url":"https://api.github.com/users/lidaof/events{/privacy}","received_events_url":"https://api.github.com/users/lidaof/received_events","type":"User","site_admin":false},"created_at":"2015-09-18T15:08:11Z","updated_at":"2015-09-18T15:08:11Z","body":"Hi @avilella, you could download from https://cgs.wustl.edu/~dli/methylQA_Download/hg38/.\r\nLet me know if you have any problem. Thanks."}}