{"action":"created","issue":{"url":"https://api.github.com/repos/leekgroup/recount-website/issues/18","repository_url":"https://api.github.com/repos/leekgroup/recount-website","labels_url":"https://api.github.com/repos/leekgroup/recount-website/issues/18/labels{/name}","comments_url":"https://api.github.com/repos/leekgroup/recount-website/issues/18/comments","events_url":"https://api.github.com/repos/leekgroup/recount-website/issues/18/events","html_url":"https://github.com/leekgroup/recount-website/issues/18","id":354664548,"node_id":"MDU6SXNzdWUzNTQ2NjQ1NDg=","number":18,"title":"prep_merge does not work for junction file","user":{"login":"gianmaz","id":42768392,"node_id":"MDQ6VXNlcjQyNzY4Mzky","avatar_url":"https://avatars1.githubusercontent.com/u/42768392?v=4","gravatar_id":"","url":"https://api.github.com/users/gianmaz","html_url":"https://github.com/gianmaz","followers_url":"https://api.github.com/users/gianmaz/followers","following_url":"https://api.github.com/users/gianmaz/following{/other_user}","gists_url":"https://api.github.com/users/gianmaz/gists{/gist_id}","starred_url":"https://api.github.com/users/gianmaz/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gianmaz/subscriptions","organizations_url":"https://api.github.com/users/gianmaz/orgs","repos_url":"https://api.github.com/users/gianmaz/repos","events_url":"https://api.github.com/users/gianmaz/events{/privacy}","received_events_url":"https://api.github.com/users/gianmaz/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":5,"created_at":"2018-08-28T10:18:47Z","updated_at":"2018-09-04T14:42:07Z","closed_at":null,"author_association":"NONE","body":"\r\nThe deliverable \"junctions.tsv.gz\" is as described in RailRNA guideline:\r\njunctions.tsv.gz: a labeled matrix whose (i, j)th element is the number of reads in sample j covering intron i. Introns are in the first column. Each one takes the form<chromosome>;<strand (+/-)>;<1-based start position (inclusive)>;<1-based end position (exclusive)>.\r\n\r\n\r\n**The following part of prep_merge.R code does not work for the junction file junctions.tsv.gz.**\r\n\r\n`## Code for creating rse_jx\r\nmessage(paste(Sys.time(), 'reading', opt$jx_file))\r\njx_info <- read.table(opt$jx_file, sep = '\\t', header = FALSE,\r\n    stringsAsFactors = FALSE, check.names = FALSE)\r\ncolnames(jx_info) <- c('chr', 'start', 'end', 'sample_ids', 'reads')\r\n\r\n## Create the counts matrix\r\nmessage(paste(Sys.time(), 'processing count information'))\r\njx_info_samples <- strsplit(jx_info$sample_ids, ',')\r\njx_info_reads <- strsplit(jx_info$reads, ',')`\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/leekgroup/recount-website/issues/comments/418393228","html_url":"https://github.com/leekgroup/recount-website/issues/18#issuecomment-418393228","issue_url":"https://api.github.com/repos/leekgroup/recount-website/issues/18","id":418393228,"node_id":"MDEyOklzc3VlQ29tbWVudDQxODM5MzIyOA==","user":{"login":"gianmaz","id":42768392,"node_id":"MDQ6VXNlcjQyNzY4Mzky","avatar_url":"https://avatars1.githubusercontent.com/u/42768392?v=4","gravatar_id":"","url":"https://api.github.com/users/gianmaz","html_url":"https://github.com/gianmaz","followers_url":"https://api.github.com/users/gianmaz/followers","following_url":"https://api.github.com/users/gianmaz/following{/other_user}","gists_url":"https://api.github.com/users/gianmaz/gists{/gist_id}","starred_url":"https://api.github.com/users/gianmaz/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gianmaz/subscriptions","organizations_url":"https://api.github.com/users/gianmaz/orgs","repos_url":"https://api.github.com/users/gianmaz/repos","events_url":"https://api.github.com/users/gianmaz/events{/privacy}","received_events_url":"https://api.github.com/users/gianmaz/received_events","type":"User","site_admin":false},"created_at":"2018-09-04T14:42:07Z","updated_at":"2018-09-04T14:42:07Z","author_association":"NONE","body":"Dear @lcolladotor and @nellore ,\r\nare there any news about the issues described in the comments above?\r\n\r\nI hope you can help me. \r\nI really need to find a quick solution to this problem.\r\nThank you.\r\nGianluca"}}
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