Dear list (and dear Nico), I encountered the following problem while annotating RNASeq reads with the UCSC table refGene (hg19): The exon coordinates of the gene model that is computed by easyRNAseq are quite different from the exon coordinates that I provide in my (self-made) annotation object. Here is one gene plus my code as an example: > # load required packages > library("easyRNASeq") > library(BSgenome.Hsapiens.UCSC.hg19) > > # get chromosome sizes > chr.sizes <- seqlengths(Hsapiens) > > # get annotation object > annot <- load("gAnnot_refGene_hg19.rda") > > # compare gene model for MYC with exons in annotation object > > object_RNASeq <- easyRNASeq(getwd(), filename = c("sample1.sorted.bam"), + readLength = 51L, + organism = "Hsapiens", + chr.sizes = chr.sizes, + format = "bam", + annotationMethod = "env", + annotationObject = exon_range, + count = "genes", + outputFormat = "RNAseq", + summarization = "geneModels" + ) > model <- geneModel(object_RNASeq) > model[which( model$gene == "MYC" ), ] # here you see the exon coordinates of the gene model RangedData with 3 rows and 4 value columns across 24 spaces space ranges | gene strand transcript <factor> <iranges> | <character> <character> <character> 1 chr8 [126085394, 126085566] | MYC + MYC_transcript 2 chr8 [126087239, 126087353] | MYC + MYC_transcript 3 chr8 [126088589, 126088742] | MYC + MYC_transcript exon <character> 1 MYC_1 2 MYC_2 3 MYC_3 > > > exon_range[which( exon_range$gene == "MYC" ), ] # here you see the exon coordinates that I provided RangedData with 3 rows and 4 value columns across 24 spaces space ranges | strand transcript gene <factor> <iranges> | <character> <character> <character> 1 chr8 [128748314, 128748869] | + NM_002467 MYC 2 chr8 [128750493, 128751265] | + NM_002467 MYC 3 chr8 [128752641, 128753680] | + NM_002467 MYC exon <character> 1 NM_002467_exon_0_0_chr8_128748315_f 2 NM_002467_exon_1_0_chr8_128750494_f 3 NM_002467_exon_2_0_chr8_128752642_f I checked genes on different chromosomes, genes with one or several exons. None of this seems to matter. What could be the problem? I am completely without a clue... Thanks a lot for any reply! Johanna -- output of sessionInfo(): R version 2.15.1 (2012-06-22) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252 LC_MONETARY=German_Germany.1252 LC_NUMERIC=C [5] LC_TIME=German_Germany.1252 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] BSgenome.Hsapiens.UCSC.hg19_1.3.19 easyRNASeq_1.4.2 ShortRead_1.16.2 latticeExtra_0.6-24 [5] RColorBrewer_1.0-5 Rsamtools_1.10.2 DESeq_1.10.1 lattice_0.20-6 [9] locfit_1.5-8 BSgenome_1.26.1 GenomicRanges_1.10.5 Biostrings_2.26.2 [13] IRanges_1.16.4 edgeR_3.0.4 limma_3.14.1 biomaRt_2.14.0 [17] Biobase_2.18.0 genomeIntervals_1.14.0 BiocGenerics_0.4.0 intervals_0.13.3 loaded via a namespace (and not attached): [1] annotate_1.36.0 AnnotationDbi_1.20.3 bitops_1.0-5 DBI_0.2-5 genefilter_1.40.0 geneplotter_1.36.0 [7] grid_2.15.1 hwriter_1.3 RCurl_1.95-3 RSQLite_0.11.2 splines_2.15.1 stats4_2.15.1 [13] survival_2.36-14 XML_3.95-0.1 xtable_1.7-0 zlibbioc_1.4.0 > -- Sent via the guest posting facility at bioconductor.org.