{"action":"created","issue":{"url":"https://api.github.com/repos/stianlagstad/chimeraviz/issues/24","repository_url":"https://api.github.com/repos/stianlagstad/chimeraviz","labels_url":"https://api.github.com/repos/stianlagstad/chimeraviz/issues/24/labels{/name}","comments_url":"https://api.github.com/repos/stianlagstad/chimeraviz/issues/24/comments","events_url":"https://api.github.com/repos/stianlagstad/chimeraviz/issues/24/events","html_url":"https://github.com/stianlagstad/chimeraviz/issues/24","id":301938347,"node_id":"MDU6SXNzdWUzMDE5MzgzNDc=","number":24,"title":"Empty reference when importing STAR-Fusion output","user":{"login":"komalsrathi","id":7000615,"node_id":"MDQ6VXNlcjcwMDA2MTU=","avatar_url":"https://avatars3.githubusercontent.com/u/7000615?v=4","gravatar_id":"","url":"https://api.github.com/users/komalsrathi","html_url":"https://github.com/komalsrathi","followers_url":"https://api.github.com/users/komalsrathi/followers","following_url":"https://api.github.com/users/komalsrathi/following{/other_user}","gists_url":"https://api.github.com/users/komalsrathi/gists{/gist_id}","starred_url":"https://api.github.com/users/komalsrathi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/komalsrathi/subscriptions","organizations_url":"https://api.github.com/users/komalsrathi/orgs","repos_url":"https://api.github.com/users/komalsrathi/repos","events_url":"https://api.github.com/users/komalsrathi/events{/privacy}","received_events_url":"https://api.github.com/users/komalsrathi/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":9,"created_at":"2018-03-02T23:29:47Z","updated_at":"2019-02-15T22:23:50Z","closed_at":null,"author_association":"NONE","body":"Hi,\r\n\r\nI am trying to import the results of STAR-Fusion (`STAR version=STAR_2.5.3a`) and facing some issues:\r\n\r\n```\r\nlibrary(chimeraviz)\r\n\r\n# Get reference to results file from deFuse\r\nsf <- importStarfusion(filename = 'star-fusion.fusion_predictions.tsv', \"hg19\", 10)\r\n\r\n# Load the results file into a list of fusion objects\r\nfusion <- getFusionByGeneName(sf, geneName = 'KANSL1')\r\nfusion <- getFusionById(fusion, id = '3')\r\n\r\n# read fastq files with reads for that fusion\r\nfastq1 <- 'SRR1559088_fusion_R1.fq'\r\nfastq2 <- 'SRR1559088_fusion_R2.fq'\r\n\r\n# extract the fusion junction sequence\r\nreferenceFilename <- \"reference.fa\"\r\nwriteFusionReference(fusion = fusion, filename = referenceFilename)\r\n```\r\n\r\nBut the reference file is empty and there are no errors associated with it. Can you have a look at this when you get a chance? \r\n\r\nHere is my sessionInfo:\r\n\r\n```\r\n> sessionInfo()\r\nR version 3.4.2 (2017-09-28)\r\nPlatform: x86_64-apple-darwin15.6.0 (64-bit)\r\nRunning under: OS X El Capitan 10.11.6\r\n\r\nMatrix products: default\r\nBLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib\r\nLAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib\r\n\r\nlocale:\r\n[1] en_US.UTF-8\r\n\r\nattached base packages:\r\n [1] grid      stats4    parallel  stats     graphics  grDevices utils     datasets \r\n [9] methods   base     \r\n\r\nother attached packages:\r\n [1] chimeraviz_1.5.4       ensembldb_2.2.2        AnnotationFilter_1.2.0\r\n [4] GenomicFeatures_1.30.3 AnnotationDbi_1.40.0   Biobase_2.38.0        \r\n [7] Gviz_1.22.3            GenomicRanges_1.30.3   GenomeInfoDb_1.14.0   \r\n[10] Biostrings_2.46.0      XVector_0.18.0         IRanges_2.12.0        \r\n[13] S4Vectors_0.16.0       BiocGenerics_0.24.0    BiocInstaller_1.28.0  \r\n\r\nloaded via a namespace (and not attached):\r\n [1] ProtGenerics_1.10.0           bitops_1.0-6                 \r\n [3] matrixStats_0.53.0            devtools_1.13.4              \r\n [5] bit64_0.9-7                   RColorBrewer_1.1-2           \r\n [7] progress_1.1.2                httr_1.3.1                   \r\n [9] rprojroot_1.3-2               tools_3.4.2                  \r\n[11] backports_1.1.2               utf8_1.1.3                   \r\n[13] DT_0.4.4                      R6_2.2.2                     \r\n[15] rpart_4.1-12                  Hmisc_4.1-1                  \r\n[17] DBI_0.7                       lazyeval_0.2.1               \r\n[19] colorspace_1.3-2              nnet_7.3-12                  \r\n[21] withr_2.1.1.9000              gridExtra_2.3                \r\n[23] prettyunits_1.0.2             RMySQL_0.10.13               \r\n[25] git2r_0.21.0                  bit_1.1-12                   \r\n[27] curl_3.1                      compiler_3.4.2               \r\n[29] cli_1.0.0                     htmlTable_1.11.2             \r\n[31] DelayedArray_0.4.1            rtracklayer_1.38.3           \r\n[33] scales_0.5.0.9000             checkmate_1.8.5              \r\n[35] readr_1.1.1                   RCircos_1.2.0                \r\n[37] stringr_1.2.0                 digest_0.6.15                \r\n[39] Rsamtools_1.30.0              foreign_0.8-69               \r\n[41] rmarkdown_1.8                 Rsubread_1.28.1              \r\n[43] pkgconfig_2.0.1               base64enc_0.1-3              \r\n[45] dichromat_2.0-0               htmltools_0.3.6              \r\n[47] highr_0.6                     BSgenome_1.46.0              \r\n[49] htmlwidgets_1.0               rlang_0.1.6.9003             \r\n[51] rstudioapi_0.7                RSQLite_2.0                  \r\n[53] shiny_1.0.5                   BiocParallel_1.12.0          \r\n[55] acepack_1.4.1                 VariantAnnotation_1.24.5     \r\n[57] RCurl_1.95-4.10               magrittr_1.5                 \r\n[59] GenomeInfoDbData_1.0.0        Formula_1.2-2                \r\n[61] Matrix_1.2-12                 Rcpp_0.12.15                 \r\n[63] munsell_0.4.3                 stringi_1.1.6                \r\n[65] yaml_2.1.16                   SummarizedExperiment_1.8.1   \r\n[67] zlibbioc_1.24.0               org.Hs.eg.db_3.5.0           \r\n[69] plyr_1.8.4                    AnnotationHub_2.10.1         \r\n[71] blob_1.1.0                    crayon_1.3.4                 \r\n[73] lattice_0.20-35               splines_3.4.2                \r\n[75] hms_0.4.1                     knitr_1.19                   \r\n[77] pillar_1.1.0                  biomaRt_2.34.2               \r\n[79] XML_3.98-1.9                  evaluate_0.10.1              \r\n[81] biovizBase_1.26.0             latticeExtra_0.6-28          \r\n[83] data.table_1.10.4-3           httpuv_1.3.5                 \r\n[85] org.Mm.eg.db_3.5.0            gtable_0.2.0                 \r\n[87] assertthat_0.2.0              ggplot2_2.2.1.9000           \r\n[89] mime_0.5                      xtable_1.8-2                 \r\n[91] ArgumentCheck_0.10.2          survival_2.41-3              \r\n[93] tibble_1.4.2                  GenomicAlignments_1.14.1     \r\n[95] memoise_1.1.0                 cluster_2.0.6                \r\n[97] interactiveDisplayBase_1.16.0 BiocStyle_2.6.1          \r\n```\r\n\r\nSTAR output files (there are four .tsv files from STAR output, you can check all four), fastq files and reference output (empty) are attached here:\r\nhttps://drive.google.com/drive/u/0/folders/1NTk0PZRMlH1KFD3xHg8_UXu5m1lmGyKj\r\n\r\nThanks!\r\n"},"comment":{"url":"https://api.github.com/repos/stianlagstad/chimeraviz/issues/comments/464226042","html_url":"https://github.com/stianlagstad/chimeraviz/issues/24#issuecomment-464226042","issue_url":"https://api.github.com/repos/stianlagstad/chimeraviz/issues/24","id":464226042,"node_id":"MDEyOklzc3VlQ29tbWVudDQ2NDIyNjA0Mg==","user":{"login":"stianlagstad","id":4340859,"node_id":"MDQ6VXNlcjQzNDA4NTk=","avatar_url":"https://avatars3.githubusercontent.com/u/4340859?v=4","gravatar_id":"","url":"https://api.github.com/users/stianlagstad","html_url":"https://github.com/stianlagstad","followers_url":"https://api.github.com/users/stianlagstad/followers","following_url":"https://api.github.com/users/stianlagstad/following{/other_user}","gists_url":"https://api.github.com/users/stianlagstad/gists{/gist_id}","starred_url":"https://api.github.com/users/stianlagstad/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/stianlagstad/subscriptions","organizations_url":"https://api.github.com/users/stianlagstad/orgs","repos_url":"https://api.github.com/users/stianlagstad/repos","events_url":"https://api.github.com/users/stianlagstad/events{/privacy}","received_events_url":"https://api.github.com/users/stianlagstad/received_events","type":"User","site_admin":false},"created_at":"2019-02-15T22:23:50Z","updated_at":"2019-02-15T22:23:50Z","author_association":"OWNER","body":"@komalsrathi Please take a look at https://github.com/stianlagstad/chimeraviz/pull/56"}}
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