Hi,
Recently, when using GRangesForUCSCGenome function with "hg19" in rtracklayer, I encountered the following error:
> targetTrack <- with(data,GRangesForUCSCGenome("hg19", chromosome, targetRanges, strand=strand, score=rate))
Error in GRangesForGenome(genome, chrom = chrom, ranges = ranges, method = "UCSC", :
Failed to obtain information for genome 'hg19'
The same script used to work two months ago. The GRangesForUCSCGenome function seems to work fine with "hg38".
It would be great if someone knows how to solve the issue.
Many thanks,
Walfred
Unable to reproduce here. Would help to see your sessionInfo() and a fully reproducible example.
Hi Michael,
Thanks for troubleshooting and, of course, the very useful rtracklayer package. Here is the sample data: https://dl.dropboxusercontent.com/s/kjaggkizixpg0uj/data.txt
Script:
> library(rtracklayer)
> data <- read.table("data.txt", sep = "\t")
> colnames(data) <- c("chromosome", "start", "end", "rate", "strand")
> targetRanges <- IRanges(data$start,data$end)
> targetTrack <- with(data,GRangesForUCSCGenome("hg19", chromosome, targetRanges, strand=strand, score=rate))
Error in GRangesForGenome(genome, chrom = chrom, ranges = ranges, method = "UCSC", :
Failed to obtain information for genome 'hg19'
> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] BSgenome.Hsapiens.UCSC.hg19_1.4.0 BSgenome_1.34.1 Biostrings_2.34.1
[4] XVector_0.6.0 rtracklayer_1.26.3 GenomicRanges_1.18.4
[7] GenomeInfoDb_1.2.5 IRanges_2.0.1 S4Vectors_0.4.0
[10] BiocGenerics_0.12.1 BiocInstaller_1.16.5
loaded via a namespace (and not attached):
[1] base64enc_0.1-3 BatchJobs_1.6 BBmisc_1.9 BiocParallel_1.0.3
[5] bitops_1.0-6 brew_1.0-6 checkmate_1.6.2 codetools_0.2-14
[9] DBI_0.3.1 digest_0.6.8 fail_1.3 foreach_1.4.2
[13] GenomicAlignments_1.2.2 iterators_1.0.7 magrittr_1.5 RCurl_1.95-4.7
[17] Rsamtools_1.18.3 RSQLite_1.0.0 sendmailR_1.2-1 stringi_0.5-5
[21] stringr_1.0.0 tools_3.1.0 XML_3.98-1.3 zlibbioc_1.12.0
As said, "hg38" works, but not "hg19". I also found that GRangesForBSGenome (instead of GRangesForUCSCGenome) works.
Many thanks,
Walfred