## ---- include = FALSE--------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, tidy = TRUE, warning=FALSE, message=FALSE, comment = "##>" ) ## ----setup-------------------------------------------------------------------- library("NanoporeRNASeq") ## ----samples------------------------------------------------------------------ data("SGNexSamples") SGNexSamples ## ----bamfiles----------------------------------------------------------------- library(ExperimentHub) NanoporeData <- query(ExperimentHub(), c("NanoporeRNA", "GRCh38","Bam")) bamFiles <- Rsamtools::BamFileList(NanoporeData[["EH3808"]], NanoporeData[["EH3809"]],NanoporeData[["EH3810"]], NanoporeData[["EH3811"]], NanoporeData[["EH3812"]], NanoporeData[["EH3813"]]) ## ----annotation--------------------------------------------------------------- data("HsChr22BambuAnnotation") HsChr22BambuAnnotation ## ---- fig.width = 8, fig.height = 6------------------------------------------- library(ggbio) range <- HsChr22BambuAnnotation$ENST00000215832 # plot mismatch track library(BSgenome.Hsapiens.NCBI.GRCh38) # plot annotation track tx <- autoplot(range, aes(col = strand), group.selfish = TRUE) # plot coverage track coverage <- autoplot(bamFiles[[1]], aes(col = coverage),which = range) #merge the tracks into one plot tracks(annotation = tx, coverage = coverage, heights = c(1, 3)) + theme_minimal() ## ----load bambu--------------------------------------------------------------- library(bambu) genomeSequenceData <- query(ExperimentHub(), c("NanoporeRNA", "GRCh38","FASTA")) genomeSequence <- genomeSequenceData[["EH7260"]] ## ---- results = "hide"-------------------------------------------------------- se <- bambu(reads = bamFiles, annotations = HsChr22BambuAnnotation, genome = genomeSequence) ## ----------------------------------------------------------------------------- se ## ---- fig.width = 8, fig.height = 10------------------------------------------ plotBambu(se, type = "annotation", gene_id = "ENSG00000099968") ## ----------------------------------------------------------------------------- sessionInfo()