{"action":"opened","issue":{"url":"https://api.github.com/repos/kcakdemir/HiCPlotter/issues/32","repository_url":"https://api.github.com/repos/kcakdemir/HiCPlotter","labels_url":"https://api.github.com/repos/kcakdemir/HiCPlotter/issues/32/labels{/name}","comments_url":"https://api.github.com/repos/kcakdemir/HiCPlotter/issues/32/comments","events_url":"https://api.github.com/repos/kcakdemir/HiCPlotter/issues/32/events","html_url":"https://github.com/kcakdemir/HiCPlotter/issues/32","id":373272084,"node_id":"MDU6SXNzdWUzNzMyNzIwODQ=","number":32,"title":"Adding gene file to HiCPlotter \"missing values\" issue","user":{"login":"awezmm","id":42984176,"node_id":"MDQ6VXNlcjQyOTg0MTc2","avatar_url":"https://avatars2.githubusercontent.com/u/42984176?v=4","gravatar_id":"","url":"https://api.github.com/users/awezmm","html_url":"https://github.com/awezmm","followers_url":"https://api.github.com/users/awezmm/followers","following_url":"https://api.github.com/users/awezmm/following{/other_user}","gists_url":"https://api.github.com/users/awezmm/gists{/gist_id}","starred_url":"https://api.github.com/users/awezmm/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/awezmm/subscriptions","organizations_url":"https://api.github.com/users/awezmm/orgs","repos_url":"https://api.github.com/users/awezmm/repos","events_url":"https://api.github.com/users/awezmm/events{/privacy}","received_events_url":"https://api.github.com/users/awezmm/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-10-24T01:55:40Z","updated_at":"2018-10-24T01:55:40Z","closed_at":null,"author_association":"NONE","body":"I input a triple sparse matrix as my hic file data. However that triple sparse matrix file represents a specific part in the genome. I then try to use -g flag to add my bed file with gene locations and I get the error: \r\n\r\nGene File (mm9-7-12-2016.bed) has some missing values\r\n\r\nThe bed file has locations of genes throughout the whole genome. However, my sparse matrix file has hic data only for a specific area in the the genome at a certain resolution. I extract my sparse file data using the straw program provided here: https://github.com/aidenlab/straw/wiki/CPP\r\n\r\nI also use the -s and -e flags to match the same start and end positions. \r\n\r\nIs the discrepancy in locations between the bed file and the sparse file the reason I am getting the error, and is there any way around it?\r\n\r\nThanks"}}
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