I just stumbled upon some oddities with rtracklayer and data generated from the NCBI/Ensembl annotation of the Drosophila genome. It seems like bigwig saved with the official NCBI/Ensembl/flybase mitochorion chromosome name dmel_mitochondrion_genome breaks the importation of a previously saved files (which does not break when loaded in other tools like the Broad IGV). Changing the chromosome name to something smaller fixes the issues. Is that a bug or it’s per design Look like a bug to me Here’s a sample script recapitulating the issue. Thanks library(GenomicFeatures) library(rtracklayer) ## Retreveing the chromsome info from BioMart chr.info <- getChromInfoFromBiomart(biomart="ensembl", dataset="dmelanogaster_gene_ensembl") ## Simulate some coverage along all the main chromsome ## Randomly distribute these 50 nt reads along the chromosomes in either orientation density <- 0.05 nreads <- sapplychr.info$length, function(length) round(rnorm(1,length*density,(length*density)*0.075))) chrs <- Rlerepchr.info$chrom,nreads)) starts <- unlist(mapply(function(n,l) ceiling((runif(n,0,l))),nreads,chr.info$length)) strands <- Rle(unlist(sapply(nreads,function(n) sample(c('+','-'),n,replace=TRUE)))) ## Create a GRanges object similuating the read positions GR <- GRanges(chrs,IRanges(starts,width=50),strands) ## Computing the coverage along the chromosomes cov <- coverage(GR) ## Saving as bigwig export(cov,'cov.bw') ## Reading back the bigwig bw <- import('cov.bw') ## This is the error I get: ## Error in .local(con, format, text, ...) : UCSC library operation failed ## In addition: Warning message: ## In .local(con, format, text, ...) : ## Value size mismatch between bptFileFind (valSize=0) and cov.bw (valSize=8) ## Replacing the name dmel_mitochondrion_genome for MT names(cov)[grep("mito",names(cov))] <- 'MT' ## Saving as bigwig export(cov,'cov_MT.bw') ## Reading back the bigwig with the modified name now works bw <- import('cov_MT.bw') —— > sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [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 attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] rtracklayer_1.22.7 GenomicFeatures_1.14.5 AnnotationDbi_1.24.0 [4] Biobase_2.22.0 GenomicRanges_1.14.4 XVector_0.2.0 [7] IRanges_1.20.7 BiocGenerics_0.8.0 loaded via a namespace (and not attached): [1] biomaRt_2.18.0 Biostrings_2.30.1 bitops_1.0-6 BSgenome_1.30.0 [5] compiler_3.0.2 DBI_0.2-7 RCurl_1.95-4.1 Rsamtools_1.14.3 [9] RSQLite_0.11.4 stats4_3.0.2 tools_3.0.2 XML_3.98-1.1 [13] zlibbioc_1.8.0 -- Marco Blanchette, Ph.D. Genomic Scientist Stowers Institute for Medical Research 1000 East 50th Street Kansas City MO 64110 www.stowers.ot Tel: 816-926-4071 Cell: 816-726-8419 Fax: 816-926-2018 [[alternative HTML version deleted]]