Run bambu
Applying bambu to bamFiles
se <- bambu(reads = bamFiles, annotations = HsChr22BambuAnnotation, genome = genomeSequence)
bambu returns a SummarizedExperiment object
se
##> class: RangedSummarizedExperiment
##> dim: 1542 6
##> metadata(2): incompatibleCounts warnings
##> assays(4): counts CPM fullLengthCounts uniqueCounts
##> rownames(1542): BambuTx1 BambuTx2 ... ENST00000641933 ENST00000641967
##> rowData names(11): TXNAME GENEID ... txid eqClassById
##> colnames(6): 96f922b312965_3844 96f9262bf7c1a_3846 ...
##> 96f921d913cf8_3852 96f923b8683e8_3854
##> colData names(1): name
Visualizing gene examples
We can visualize the annotated and novel isoforms identified in this gene example using plot functions from bambu
plotBambu(se, type = "annotation", gene_id = "ENSG00000099968")
##> [[1]]
##> TableGrob (3 x 1) "arrange": 3 grobs
##> z cells name grob
##> 1 1 (2-2,1-1) arrange gtable[layout]
##> 2 2 (3-3,1-1) arrange gtable[layout]
##> 3 3 (1-1,1-1) arrange text[GRID.text.248]
sessionInfo()
##> R version 4.3.1 (2023-06-16)
##> Platform: x86_64-pc-linux-gnu (64-bit)
##> Running under: Ubuntu 22.04.3 LTS
##>
##> Matrix products: default
##> BLAS: /home/biocbuild/bbs-3.18-bioc/R/lib/libRblas.so
##> LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
##>
##> locale:
##> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
##> [3] LC_TIME=en_GB LC_COLLATE=C
##> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
##> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
##> [9] LC_ADDRESS=C LC_TELEPHONE=C
##> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##>
##> time zone: America/New_York
##> tzcode source: system (glibc)
##>
##> attached base packages:
##> [1] stats4 stats graphics grDevices utils datasets methods
##> [8] base
##>
##> other attached packages:
##> [1] bambu_3.4.0
##> [2] SummarizedExperiment_1.32.0
##> [3] Biobase_2.62.0
##> [4] MatrixGenerics_1.14.0
##> [5] matrixStats_1.0.0
##> [6] BSgenome.Hsapiens.NCBI.GRCh38_1.3.1000
##> [7] BSgenome_1.70.0
##> [8] rtracklayer_1.62.0
##> [9] BiocIO_1.12.0
##> [10] ggbio_1.50.0
##> [11] ggplot2_3.4.4
##> [12] Rsamtools_2.18.0
##> [13] Biostrings_2.70.1
##> [14] XVector_0.42.0
##> [15] GenomicRanges_1.54.0
##> [16] GenomeInfoDb_1.38.0
##> [17] IRanges_2.36.0
##> [18] S4Vectors_0.40.0
##> [19] NanoporeRNASeq_1.12.0
##> [20] ExperimentHub_2.10.0
##> [21] AnnotationHub_3.10.0
##> [22] BiocFileCache_2.10.0
##> [23] dbplyr_2.3.4
##> [24] BiocGenerics_0.48.0
##>
##> loaded via a namespace (and not attached):
##> [1] RColorBrewer_1.1-3 rstudioapi_0.15.0
##> [3] jsonlite_1.8.7 magrittr_2.0.3
##> [5] GenomicFeatures_1.54.0 farver_2.1.1
##> [7] rmarkdown_2.25 zlibbioc_1.48.0
##> [9] vctrs_0.6.4 memoise_2.0.1
##> [11] RCurl_1.98-1.12 base64enc_0.1-3
##> [13] htmltools_0.5.6.1 S4Arrays_1.2.0
##> [15] progress_1.2.2 curl_5.1.0
##> [17] xgboost_1.7.5.1 SparseArray_1.2.0
##> [19] Formula_1.2-5 sass_0.4.7
##> [21] bslib_0.5.1 htmlwidgets_1.6.2
##> [23] plyr_1.8.9 cachem_1.0.8
##> [25] GenomicAlignments_1.38.0 mime_0.12
##> [27] lifecycle_1.0.3 pkgconfig_2.0.3
##> [29] Matrix_1.6-1.1 R6_2.5.1
##> [31] fastmap_1.1.1 GenomeInfoDbData_1.2.11
##> [33] shiny_1.7.5.1 digest_0.6.33
##> [35] colorspace_2.1-0 GGally_2.1.2
##> [37] reshape_0.8.9 OrganismDbi_1.44.0
##> [39] AnnotationDbi_1.64.0 Hmisc_5.1-1
##> [41] RSQLite_2.3.1 labeling_0.4.3
##> [43] filelock_1.0.2 fansi_1.0.5
##> [45] httr_1.4.7 abind_1.4-5
##> [47] compiler_4.3.1 bit64_4.0.5
##> [49] withr_2.5.1 htmlTable_2.4.1
##> [51] backports_1.4.1 BiocParallel_1.36.0
##> [53] DBI_1.1.3 biomaRt_2.58.0
##> [55] rappdirs_0.3.3 DelayedArray_0.28.0
##> [57] rjson_0.2.21 tools_4.3.1
##> [59] foreign_0.8-85 interactiveDisplayBase_1.40.0
##> [61] httpuv_1.6.12 nnet_7.3-19
##> [63] glue_1.6.2 restfulr_0.0.15
##> [65] promises_1.2.1 grid_4.3.1
##> [67] checkmate_2.3.0 cluster_2.1.4
##> [69] reshape2_1.4.4 generics_0.1.3
##> [71] gtable_0.3.4 tidyr_1.3.0
##> [73] ensembldb_2.26.0 data.table_1.14.8
##> [75] hms_1.1.3 xml2_1.3.5
##> [77] utf8_1.2.4 BiocVersion_3.18.0
##> [79] pillar_1.9.0 stringr_1.5.0
##> [81] later_1.3.1 dplyr_1.1.3
##> [83] lattice_0.22-5 bit_4.0.5
##> [85] biovizBase_1.50.0 RBGL_1.78.0
##> [87] tidyselect_1.2.0 knitr_1.44
##> [89] gridExtra_2.3 ProtGenerics_1.34.0
##> [91] xfun_0.40 stringi_1.7.12
##> [93] lazyeval_0.2.2 yaml_2.3.7
##> [95] evaluate_0.22 codetools_0.2-19
##> [97] tibble_3.2.1 graph_1.80.0
##> [99] BiocManager_1.30.22 cli_3.6.1
##> [101] rpart_4.1.21 xtable_1.8-4
##> [103] munsell_0.5.0 jquerylib_0.1.4
##> [105] dichromat_2.0-0.1 Rcpp_1.0.11
##> [107] png_0.1-8 XML_3.99-0.14
##> [109] parallel_4.3.1 ellipsis_0.3.2
##> [111] blob_1.2.4 prettyunits_1.2.0
##> [113] AnnotationFilter_1.26.0 bitops_1.0-7
##> [115] VariantAnnotation_1.48.0 scales_1.2.1
##> [117] purrr_1.0.2 crayon_1.5.2
##> [119] rlang_1.1.1 KEGGREST_1.42.0
##> [121] formatR_1.14
