{"action":"created","issue":{"url":"https://api.github.com/repos/CGATOxford/UMI-tools/issues/177","repository_url":"https://api.github.com/repos/CGATOxford/UMI-tools","labels_url":"https://api.github.com/repos/CGATOxford/UMI-tools/issues/177/labels{/name}","comments_url":"https://api.github.com/repos/CGATOxford/UMI-tools/issues/177/comments","events_url":"https://api.github.com/repos/CGATOxford/UMI-tools/issues/177/events","html_url":"https://github.com/CGATOxford/UMI-tools/pull/177","id":255360072,"number":177,"title":"Added new tool \"tabulate\" which output a table of all (grouped) UMIs and their read counts","user":{"login":"fgp","id":163875,"avatar_url":"https://avatars3.githubusercontent.com/u/163875?v=4","gravatar_id":"","url":"https://api.github.com/users/fgp","html_url":"https://github.com/fgp","followers_url":"https://api.github.com/users/fgp/followers","following_url":"https://api.github.com/users/fgp/following{/other_user}","gists_url":"https://api.github.com/users/fgp/gists{/gist_id}","starred_url":"https://api.github.com/users/fgp/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/fgp/subscriptions","organizations_url":"https://api.github.com/users/fgp/orgs","repos_url":"https://api.github.com/users/fgp/repos","events_url":"https://api.github.com/users/fgp/events{/privacy}","received_events_url":"https://api.github.com/users/fgp/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2017-09-05T17:59:06Z","updated_at":"2017-09-06T15:44:08Z","closed_at":null,"author_association":"NONE","pull_request":{"url":"https://api.github.com/repos/CGATOxford/UMI-tools/pulls/177","html_url":"https://github.com/CGATOxford/UMI-tools/pull/177","diff_url":"https://github.com/CGATOxford/UMI-tools/pull/177.diff","patch_url":"https://github.com/CGATOxford/UMI-tools/pull/177.patch"},"body":"Hi,\r\n\r\nThis is kind of a hybrid of \"group\" and \"count\". For my project, I need to get the (summed) read-counts for each group of merged UMIs. \"count\" throws away too much information to be useful to me -- it reports only the per-gene total UMI count. \"group\", on the other hand, does too little -- it only groups reads, but would leave it to me to associate them to gene and to sum read counts over groups of reads with similar UMIs. Until now, I used a custom python script that did a job similar to what UMI-Tools does. To be able to switch over to UMI-Tools, I implemented the \"tabulate\" mode which outputs exactly what I need. It produces a table with one row per UMI-group, showing the gene and cell (if applicable), as well as the most common start and end mapping positions, total read count, and number of distinct UMIs in the group.\r\n\r\nI'd love to see this integraded in UMI-Tools. This pull request contains a first stab at an implementation. It works, but isn't perfect yet. For one, it lacks documentation. And it needs to access both reads of a mate pair to correctly compute start and end mapping positions (because, like the rest of UMI-Tools, it attempts to take clipping into account). The lack of documentation I'll address soonish. For the 2nd problem I don't have a good solution yet. I'm sending this pull request not because I expect this to be merged in its current form (at least the documentation should be there, I gess), but because I wanted to have feedback on whether you'd consider merging this feature at all, and whether the approach I took is acceptable.\r\n\r\nbest,\r\nFlorian"},"comment":{"url":"https://api.github.com/repos/CGATOxford/UMI-tools/issues/comments/327525919","html_url":"https://github.com/CGATOxford/UMI-tools/pull/177#issuecomment-327525919","issue_url":"https://api.github.com/repos/CGATOxford/UMI-tools/issues/177","id":327525919,"user":{"login":"fgp","id":163875,"avatar_url":"https://avatars3.githubusercontent.com/u/163875?v=4","gravatar_id":"","url":"https://api.github.com/users/fgp","html_url":"https://github.com/fgp","followers_url":"https://api.github.com/users/fgp/followers","following_url":"https://api.github.com/users/fgp/following{/other_user}","gists_url":"https://api.github.com/users/fgp/gists{/gist_id}","starred_url":"https://api.github.com/users/fgp/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/fgp/subscriptions","organizations_url":"https://api.github.com/users/fgp/orgs","repos_url":"https://api.github.com/users/fgp/repos","events_url":"https://api.github.com/users/fgp/events{/privacy}","received_events_url":"https://api.github.com/users/fgp/received_events","type":"User","site_admin":false},"created_at":"2017-09-06T15:44:08Z","updated_at":"2017-09-06T15:44:08Z","author_association":"NONE","body":"That /dev/stdout trick looks neat, I'll try that! Eventually to fully replace my existing pipeline I will need \"end\" and \"cell\" columns. But for now I can do without them. The cell column looks easy to add. For the end column, I think a clean solution would require extending bundle_iterator to collect and hand back both reads of a mate pair, instead of just the first."}}
{"actor":{"display_login":"fgp"}}