{"action":"created","issue":{"url":"https://api.github.com/repos/satijalab/seurat/issues/1171","repository_url":"https://api.github.com/repos/satijalab/seurat","labels_url":"https://api.github.com/repos/satijalab/seurat/issues/1171/labels{/name}","comments_url":"https://api.github.com/repos/satijalab/seurat/issues/1171/comments","events_url":"https://api.github.com/repos/satijalab/seurat/issues/1171/events","html_url":"https://github.com/satijalab/seurat/issues/1171","id":413230948,"node_id":"MDU6SXNzdWU0MTMyMzA5NDg=","number":1171,"title":"problem with loading data generated by Cell ranger v3","user":{"login":"shendong124","id":29153026,"node_id":"MDQ6VXNlcjI5MTUzMDI2","avatar_url":"https://avatars3.githubusercontent.com/u/29153026?v=4","gravatar_id":"","url":"https://api.github.com/users/shendong124","html_url":"https://github.com/shendong124","followers_url":"https://api.github.com/users/shendong124/followers","following_url":"https://api.github.com/users/shendong124/following{/other_user}","gists_url":"https://api.github.com/users/shendong124/gists{/gist_id}","starred_url":"https://api.github.com/users/shendong124/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/shendong124/subscriptions","organizations_url":"https://api.github.com/users/shendong124/orgs","repos_url":"https://api.github.com/users/shendong124/repos","events_url":"https://api.github.com/users/shendong124/events{/privacy}","received_events_url":"https://api.github.com/users/shendong124/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2019-02-22T03:50:03Z","updated_at":"2019-02-22T14:18:03Z","closed_at":null,"author_association":"NONE","body":"Hi ,\r\nI have successfully installed Seurat v3:\r\n\r\n> packageVersion(pkg = \"Seurat\")\r\n[1] ‘3.0.0.9000’\r\n\r\nBut here is what I get when I am trying to load the data:\r\n\r\n> CD3_CR3_2.data <- Read10X(data.dir = \"~shendong/Desktop/CD3_GEX_CR3filt\")\r\nError in Read10X(data.dir = \"~shendong/Desktop/CD3_GEX_CR3filt\") : \r\n  Gene name file missing\r\n\r\nThe problem that I see is the path of filtered_bc_matrices generated by Cellranger3 is:\r\n/outs/filtered_feature_bc_matrix/barcodes.tsv.gz \r\n/outs/filtered_feature_bc_matrix/features.tsv.gz  \r\n/outs/filtered_feature_bc_matrix/matrix.mtx.gz\r\n\r\nI could go further in the analysis by opening the gz files and changing the name of features.tsv to gene.tsv but at the next step:\r\n\r\npbmc <- CreateSeuratObject(counts = pbmc.data, min.cells = 3, min.features = 200, project = \"10X_PBMC\")\r\n\r\nI have the following error:\r\n\r\nError in new(Class = \"seurat\", raw.data = raw.data, is.expr = is.expr,  : \r\n  argument \"raw.data\" is missing, with no default\r\nIn addition: Warning messages:\r\n1: In mget(objectNames, envir = ns, inherits = TRUE) :\r\n  restarting interrupted promise evaluation\r\n2: In mget(objectNames, envir = ns, inherits = TRUE) :\r\n  internal error -3 in R_decompress1\r\n3: In mget(objectNames, envir = ns, inherits = TRUE) :\r\n  restarting interrupted promise evaluation\r\n4: In mget(objectNames, envir = ns, inherits = TRUE) :\r\n  internal error -3 in R_decompress1\r\n\r\nThe problem I think comes from the fact that data generated from cell ranger 3 is not the usual format outs/filtered_gene_bc_matrices/GRCh38/(barcodes.tsv  genes.tsv  matrix.mtx) but look like this:\r\n\r\n/outs/filtered_feature_bc_matrix/barcodes.tsv.gz \r\n/outs/filtered_feature_bc_matrix/features.tsv.gz  \r\n/outs/filtered_feature_bc_matrix/matrix.mtx.gz\r\n\r\nIt is probably a very simple thing that I am missing but I am very new at this and would appreciate some guidance.\r\n\r\nThank you very much for your help!\r\n\r\n\r\n\r\n\r\n\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/satijalab/seurat/issues/comments/466410895","html_url":"https://github.com/satijalab/seurat/issues/1171#issuecomment-466410895","issue_url":"https://api.github.com/repos/satijalab/seurat/issues/1171","id":466410895,"node_id":"MDEyOklzc3VlQ29tbWVudDQ2NjQxMDg5NQ==","user":{"login":"timoast","id":4591688,"node_id":"MDQ6VXNlcjQ1OTE2ODg=","avatar_url":"https://avatars2.githubusercontent.com/u/4591688?v=4","gravatar_id":"","url":"https://api.github.com/users/timoast","html_url":"https://github.com/timoast","followers_url":"https://api.github.com/users/timoast/followers","following_url":"https://api.github.com/users/timoast/following{/other_user}","gists_url":"https://api.github.com/users/timoast/gists{/gist_id}","starred_url":"https://api.github.com/users/timoast/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/timoast/subscriptions","organizations_url":"https://api.github.com/users/timoast/orgs","repos_url":"https://api.github.com/users/timoast/repos","events_url":"https://api.github.com/users/timoast/events{/privacy}","received_events_url":"https://api.github.com/users/timoast/received_events","type":"User","site_admin":false},"created_at":"2019-02-22T14:18:03Z","updated_at":"2019-02-22T14:18:03Z","author_association":"COLLABORATOR","body":"It looks like you still have version 2 loaded. Try restarting your R session and verifying that Seurat v3 is loaded by running `sessionInfo()` before running the commands."}}
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