{"action":"created","comment":{"url":"https://api.github.com/repos/galaxyproject/training-material/pulls/comments/221424783","pull_request_review_id":160077196,"id":221424783,"node_id":"MDI0OlB1bGxSZXF1ZXN0UmV2aWV3Q29tbWVudDIyMTQyNDc4Mw==","diff_hunk":"@@ -349,35 +358,27 @@ you want to include Transcriptions factors in ChIP-seq experiments.\n > 3. Rename your dataset to reflect your findings\n {: .hands_on}\n \n-You might have noticed that the UCSC file is in `BED` format and has a database associated to it. That's what we want for our peak file as well","path":"topics/introduction/tutorials/galaxy-intro-peaks2genes/tutorial.md","position":109,"original_position":55,"commit_id":"6e30cd39009b0c6dd614dba57aa111f0b5593a32","original_commit_id":"e04b1d0afe0e9cab04f3a1fa89194673e5ee5003","user":{"login":"bgruening","id":469983,"node_id":"MDQ6VXNlcjQ2OTk4Mw==","avatar_url":"https://avatars2.githubusercontent.com/u/469983?v=4","gravatar_id":"","url":"https://api.github.com/users/bgruening","html_url":"https://github.com/bgruening","followers_url":"https://api.github.com/users/bgruening/followers","following_url":"https://api.github.com/users/bgruening/following{/other_user}","gists_url":"https://api.github.com/users/bgruening/gists{/gist_id}","starred_url":"https://api.github.com/users/bgruening/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bgruening/subscriptions","organizations_url":"https://api.github.com/users/bgruening/orgs","repos_url":"https://api.github.com/users/bgruening/repos","events_url":"https://api.github.com/users/bgruening/events{/privacy}","received_events_url":"https://api.github.com/users/bgruening/received_events","type":"User","site_admin":false},"body":"I disagree here. The `Get Flanks` tool is also not needed as a similar result can be archived by UCSC directly. It's important that people know the interface and this is the purpose of this tutorial, it's an introduction to Galaxy. \r\nAlso please note that they are different intersect tools in Galaxy and not all can cope with interval files and hence convert them implicitly. It's therefore good to know that there are implicit and explicit conversions, maybe this should be made more clear in the text - I stress this a lot during my session.\r\n\r\nThanks for adding it back. ","created_at":"2018-09-29T11:04:14Z","updated_at":"2018-09-29T11:04:14Z","html_url":"https://github.com/galaxyproject/training-material/pull/1030#discussion_r221424783","pull_request_url":"https://api.github.com/repos/galaxyproject/training-material/pulls/1030","author_association":"MEMBER","_links":{"self":{"href":"https://api.github.com/repos/galaxyproject/training-material/pulls/comments/221424783"},"html":{"href":"https://github.com/galaxyproject/training-material/pull/1030#discussion_r221424783"},"pull_request":{"href":"https://api.github.com/repos/galaxyproject/training-material/pulls/1030"}},"in_reply_to_id":221421323},"pull_request":{"url":"https://api.github.com/repos/galaxyproject/training-material/pulls/1030","id":218906507,"node_id":"MDExOlB1bGxSZXF1ZXN0MjE4OTA2NTA3","html_url":"https://github.com/galaxyproject/training-material/pull/1030","diff_url":"https://github.com/galaxyproject/training-material/pull/1030.diff","patch_url":"https://github.com/galaxyproject/training-material/pull/1030.patch","issue_url":"https://api.github.com/repos/galaxyproject/training-material/issues/1030","number":1030,"state":"open","locked":false,"title":"Peaks2genes: modifications","user":{"login":"mblue9","id":5591821,"node_id":"MDQ6VXNlcjU1OTE4MjE=","avatar_url":"https://avatars0.githubusercontent.com/u/5591821?v=4","gravatar_id":"","url":"https://api.github.com/users/mblue9","html_url":"https://github.com/mblue9","followers_url":"https://api.github.com/users/mblue9/followers","following_url":"https://api.github.com/users/mblue9/following{/other_user}","gists_url":"https://api.github.com/users/mblue9/gists{/gist_id}","starred_url":"https://api.github.com/users/mblue9/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mblue9/subscriptions","organizations_url":"https://api.github.com/users/mblue9/orgs","repos_url":"https://api.github.com/users/mblue9/repos","events_url":"https://api.github.com/users/mblue9/events{/privacy}","received_events_url":"https://api.github.com/users/mblue9/received_events","type":"User","site_admin":false},"body":"In response to [this feedback comment](https://github.com/galaxyproject/training-material/issues/989#issuecomment-422013694) on the peaks to genes tutorial:\r\n\r\n>What could be improved?: More information on the flanking region tool (how it works)\r\n\r\nI've tried to clarify in this PR what the Get Flanks tool is doing in the text and I've added in a small diagram (made with Powerpoint 😳if there's a better way to make one please let me know).\r\n\r\nI've made a few changes here:\r\n\r\n* Tried to clarify Get Flanks step \r\n* I get chromosome 11 having the highest no. of genes (not chr 7) using the provided files (?) so have changed that in the text\r\n* Added steps to add tags to the inputs (peaks and genes) as that makes it easier to see (for me anyway) which data the Replace/Cut etc outputs are \r\n* Removed the Convert Genomic Intervals to Bed step as it doesn't seem necessary, Intersect gives the same output without that step. Converting the the peaks file to bed also looks weird to me, as it's not bed format, it's just a table e.g. there's no Strand column and when you convert to bed a numeric column ends up being called \"Strand\" ) so Interval looks better I think\r\n* Added some screenshots to clarify some expected outputs","created_at":"2018-09-28T09:27:58Z","updated_at":"2018-09-29T11:04:14Z","closed_at":null,"merged_at":null,"merge_commit_sha":"c8af8b55c45cc7d21eaa610df5bacf65397e98dd","assignee":null,"assignees":[],"requested_reviewers":[],"requested_teams":[],"labels":[{"id":450570170,"node_id":"MDU6TGFiZWw0NTA1NzAxNzA=","url":"https://api.github.com/repos/galaxyproject/training-material/labels/topic:%20introduction","name":"topic: 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