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): d7f6f2b7a8900_3844 d7f6f1db70868_3846 ...
##> d7f6f339919da_3852 d7f6f57afd7ec_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 (4 x 1) "arrange": 4 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 (4-4,1-1) arrange gtable[layout]
##> 4 4 (1-1,1-1) arrange text[GRID.text.281]
sessionInfo()
##> R version 4.5.0 beta (2025-04-02 r88102)
##> Platform: x86_64-pc-linux-gnu
##> Running under: Ubuntu 24.04.2 LTS
##>
##> Matrix products: default
##> BLAS: /home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so
##> LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0 LAPACK version 3.12.0
##>
##> 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_3.11.0
##> [2] SummarizedExperiment_1.39.0
##> [3] Biobase_2.69.0
##> [4] MatrixGenerics_1.21.0
##> [5] matrixStats_1.5.0
##> [6] BSgenome.Hsapiens.NCBI.GRCh38_1.3.1000
##> [7] BSgenome_1.77.0
##> [8] rtracklayer_1.69.0
##> [9] BiocIO_1.19.0
##> [10] ggbio_1.57.0
##> [11] ggplot2_3.5.2
##> [12] Rsamtools_2.25.0
##> [13] Biostrings_2.77.0
##> [14] XVector_0.49.0
##> [15] GenomicRanges_1.61.0
##> [16] GenomeInfoDb_1.45.0
##> [17] IRanges_2.43.0
##> [18] S4Vectors_0.47.0
##> [19] NanoporeRNASeq_1.19.0
##> [20] ExperimentHub_2.17.0
##> [21] AnnotationHub_3.17.0
##> [22] BiocFileCache_2.17.0
##> [23] dbplyr_2.5.0
##> [24] BiocGenerics_0.55.0
##> [25] generics_0.1.3
##>
##> loaded via a namespace (and not attached):
##> [1] RColorBrewer_1.1-3 rstudioapi_0.17.1 jsonlite_2.0.0
##> [4] magrittr_2.0.3 GenomicFeatures_1.61.0 farver_2.1.2
##> [7] rmarkdown_2.29 vctrs_0.6.5 memoise_2.0.1
##> [10] RCurl_1.98-1.17 base64enc_0.1-3 htmltools_0.5.8.1
##> [13] S4Arrays_1.9.0 progress_1.2.3 curl_6.2.2
##> [16] xgboost_1.7.9.1 SparseArray_1.9.0 Formula_1.2-5
##> [19] sass_0.4.10 bslib_0.9.0 htmlwidgets_1.6.4
##> [22] plyr_1.8.9 httr2_1.1.2 cachem_1.1.0
##> [25] GenomicAlignments_1.45.0 mime_0.13 lifecycle_1.0.4
##> [28] pkgconfig_2.0.3 Matrix_1.7-3 R6_2.6.1
##> [31] fastmap_1.2.0 GenomeInfoDbData_1.2.14 digest_0.6.37
##> [34] colorspace_2.1-1 GGally_2.2.1 AnnotationDbi_1.71.0
##> [37] OrganismDbi_1.51.0 Hmisc_5.2-3 RSQLite_2.3.9
##> [40] labeling_0.4.3 filelock_1.0.3 httr_1.4.7
##> [43] abind_1.4-8 compiler_4.5.0 bit64_4.6.0-1
##> [46] withr_3.0.2 htmlTable_2.4.3 backports_1.5.0
##> [49] BiocParallel_1.43.0 DBI_1.2.3 ggstats_0.9.0
##> [52] biomaRt_2.65.0 rappdirs_0.3.3 DelayedArray_0.35.0
##> [55] rjson_0.2.23 tools_4.5.0 foreign_0.8-90
##> [58] nnet_7.3-20 glue_1.8.0 restfulr_0.0.15
##> [61] grid_4.5.0 checkmate_2.3.2 cluster_2.1.8.1
##> [64] reshape2_1.4.4 gtable_0.3.6 tidyr_1.3.1
##> [67] ensembldb_2.33.0 data.table_1.17.0 hms_1.1.3
##> [70] xml2_1.3.8 BiocVersion_3.22.0 pillar_1.10.2
##> [73] stringr_1.5.1 dplyr_1.1.4 lattice_0.22-7
##> [76] bit_4.6.0 biovizBase_1.57.0 RBGL_1.85.0
##> [79] tidyselect_1.2.1 knitr_1.50 gridExtra_2.3
##> [82] ProtGenerics_1.41.0 xfun_0.52 stringi_1.8.7
##> [85] UCSC.utils_1.5.0 lazyeval_0.2.2 yaml_2.3.10
##> [88] evaluate_1.0.3 codetools_0.2-20 tibble_3.2.1
##> [91] graph_1.87.0 BiocManager_1.30.25 cli_3.6.4
##> [94] rpart_4.1.24 munsell_0.5.1 jquerylib_0.1.4
##> [97] dichromat_2.0-0.1 Rcpp_1.0.14 png_0.1-8
##> [100] XML_3.99-0.18 parallel_4.5.0 blob_1.2.4
##> [103] prettyunits_1.2.0 AnnotationFilter_1.33.0 bitops_1.0-9
##> [106] txdbmaker_1.5.0 VariantAnnotation_1.55.0 scales_1.3.0
##> [109] purrr_1.0.4 crayon_1.5.3 rlang_1.1.6
##> [112] KEGGREST_1.49.0 formatR_1.14
