{"action":"created","issue":{"url":"https://api.github.com/repos/deeptools/deepTools/issues/689","repository_url":"https://api.github.com/repos/deeptools/deepTools","labels_url":"https://api.github.com/repos/deeptools/deepTools/issues/689/labels{/name}","comments_url":"https://api.github.com/repos/deeptools/deepTools/issues/689/comments","events_url":"https://api.github.com/repos/deeptools/deepTools/issues/689/events","html_url":"https://github.com/deeptools/deepTools/issues/689","id":309180340,"number":689,"title":"Visualizing ChIPSeqData ","user":{"login":"sengoku93","id":37084775,"avatar_url":"https://avatars3.githubusercontent.com/u/37084775?v=4","gravatar_id":"","url":"https://api.github.com/users/sengoku93","html_url":"https://github.com/sengoku93","followers_url":"https://api.github.com/users/sengoku93/followers","following_url":"https://api.github.com/users/sengoku93/following{/other_user}","gists_url":"https://api.github.com/users/sengoku93/gists{/gist_id}","starred_url":"https://api.github.com/users/sengoku93/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sengoku93/subscriptions","organizations_url":"https://api.github.com/users/sengoku93/orgs","repos_url":"https://api.github.com/users/sengoku93/repos","events_url":"https://api.github.com/users/sengoku93/events{/privacy}","received_events_url":"https://api.github.com/users/sengoku93/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":11,"created_at":"2018-03-28T00:33:09Z","updated_at":"2018-03-29T15:16:39Z","closed_at":"2018-03-29T12:35:56Z","author_association":"NONE","body":"Hi,\r\n\r\nI am currently trying to generate peakcentered ChIP seq heatmaps. However, I'm having trouble generating these heatmaps because the resulting heat map  has a single value per gene (one specific color) rather than several values per gene dependent on bin size (therefore multiple colors per row). Below are the multiple commands I tried (all resulting in similar heatmap that is attached, cropped image)(I also attached a representative example of the type of heatmap I'd like to generate, called represenative heatmap):\r\n\r\n**bamCoverage:**\r\n\r\nbamCoverage -b input.bam -o output.bw  \r\nbamCoverage -b input.bam -o output.bw --centerReads\r\n\r\n**Compute Matrix:**\r\n\r\ncomputeMatrix reference-point -S input.bw  -R gencode.v19.annotation.gtf  --referencePoint center --sortRegions keep -a 1000 -b 1000 -bs 50 -o output.gz\r\n\r\ncomputeMatrix reference-point -S input.bw  -R gencode.v19.annotation.gtf  --referencePoint center --sortRegions keep -a 1000 -b 1000 -bs 10 -o output.gz\r\n\r\n**plotHeatmap:**\r\n\r\nplotHeatmap -m p63 input.gz  -out ouput_v19.png --sortRegions no --colorMap 'RdBu'\r\n\r\nAny help would be appreciated! Thank you!\r\n\r\n-sengoku\r\n\r\n![10bp_v19_cropped](https://user-images.githubusercontent.com/37084775/38001840-1789406a-31fd-11e8-870b-1fa862213aea.png)\r\n\r\n<img width=\"188\" alt=\"representative heatmap\" src=\"https://user-images.githubusercontent.com/37084775/38001996-dd943f62-31fd-11e8-9259-68853b8d15b5.png\">\r\n\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/deeptools/deepTools/issues/comments/377269357","html_url":"https://github.com/deeptools/deepTools/issues/689#issuecomment-377269357","issue_url":"https://api.github.com/repos/deeptools/deepTools/issues/689","id":377269357,"user":{"login":"sengoku93","id":37084775,"avatar_url":"https://avatars3.githubusercontent.com/u/37084775?v=4","gravatar_id":"","url":"https://api.github.com/users/sengoku93","html_url":"https://github.com/sengoku93","followers_url":"https://api.github.com/users/sengoku93/followers","following_url":"https://api.github.com/users/sengoku93/following{/other_user}","gists_url":"https://api.github.com/users/sengoku93/gists{/gist_id}","starred_url":"https://api.github.com/users/sengoku93/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sengoku93/subscriptions","organizations_url":"https://api.github.com/users/sengoku93/orgs","repos_url":"https://api.github.com/users/sengoku93/repos","events_url":"https://api.github.com/users/sengoku93/events{/privacy}","received_events_url":"https://api.github.com/users/sengoku93/received_events","type":"User","site_admin":false},"created_at":"2018-03-29T15:16:39Z","updated_at":"2018-03-29T15:16:39Z","author_association":"NONE","body":"Therefore, instead of the gencodev19 I would use a bed file generate from Macs2 peak calling? thank you"}}
{"actor":{"display_login":"sengoku93"}}