The line below gives Bad Request message..
ideoTrack <- ideogramTrack(genome="hg19", chromosome="chrX")
I tried UCSC mirror just in case, but still gave same error
options(Gviz.ucscUrl="http://genome-euro.ucsc.edu/cgi-bin/")
Is there a change in UCSC API or update in URLs?
I have just try it on both release and developmental version and both works for me. In fact I used "IdeogramTrack" but I assume that was just a typo in your post. Could it be, that you are being firewall or proxy?
Hi Robert, Thanks for the answer.. As far as I know I'm not behind firewall or proxy. In the code below, biomart query works but Ideogram track query does not work.
```{r}
library(Gviz)
library(biomaRt)
chr <- "chr5"
start<-170814000
end<-170815000
gtrack <- GenomeAxisTrack()
ideoTrack <- IdeogramTrack(genome = "hg19", chromosome = chr)
bmt <- BiomartGeneRegionTrack(genome = "hg19", chromosome = chr, start = start, end = end, filter = list(with_ox_refseq_mrna = TRUE), stacking = "dense")
```
Below is the traceback output of the error. How can I debug or troubleshoot this problem?
(If image embedding does not work here's the link https://pasteboard.co/H5rymfx.png)
Sorry about that, I completely forgot about it. Here's the session info:
R version 3.4.1 (2017-06-30) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Debian GNU/Linux 9 (stretch) Matrix products: default BLAS/LAPACK: /usr/lib/libopenblasp-r0.2.19.so locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=C [7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] grid parallel stats4 stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_2.34.0 Gviz_1.22.0 GenomicRanges_1.30.0 GenomeInfoDb_1.14.0 IRanges_2.12.0 [6] S4Vectors_0.16.0 BiocGenerics_0.24.0 loaded via a namespace (and not attached): [1] httr_1.3.1 Biobase_2.38.0 RMySQL_0.10.13 [4] AnnotationHub_2.10.1 bit64_0.9-7 splines_3.4.1 [7] shiny_1.0.5 Formula_1.2-2 assertthat_0.2.0 [10] interactiveDisplayBase_1.16.0 latticeExtra_0.6-28 blob_1.1.0 [13] BSgenome_1.46.0 GenomeInfoDbData_0.99.1 Rsamtools_1.30.0 [16] yaml_2.1.14 progress_1.1.2 RSQLite_2.0 [19] backports_1.1.1 lattice_0.20-35 biovizBase_1.26.0 [22] digest_0.6.12 RColorBrewer_1.1-2 XVector_0.18.0 [25] checkmate_1.8.5 colorspace_1.3-2 httpuv_1.3.5 [28] htmltools_0.3.6 Matrix_1.2-12 plyr_1.8.4 [31] XML_3.98-1.9 zlibbioc_1.24.0 xtable_1.8-2 [34] scales_0.5.0 BiocParallel_1.12.0 htmlTable_1.9 [37] tibble_1.3.4 AnnotationFilter_1.2.0 ggplot2_2.2.1 [40] SummarizedExperiment_1.8.0 GenomicFeatures_1.30.0 nnet_7.3-12 [43] lazyeval_0.2.1 mime_0.5 survival_2.41-3 [46] magrittr_1.5 memoise_1.1.0 foreign_0.8-69 [49] BiocInstaller_1.28.0 tools_3.4.1 data.table_1.10.4-3 [52] prettyunits_1.0.2 matrixStats_0.52.2 stringr_1.2.0 [55] munsell_0.4.3 cluster_2.0.6 DelayedArray_0.4.1 [58] AnnotationDbi_1.40.0 ensembldb_2.2.0 Biostrings_2.46.0 [61] compiler_3.4.1 rlang_0.1.4 RCurl_1.95-4.8 [64] dichromat_2.0-0 VariantAnnotation_1.24.1 htmlwidgets_0.9 [67] bitops_1.0-6 base64enc_0.1-3 gtable_0.2.0 [70] curl_3.0 DBI_0.7 R6_2.2.2 [73] GenomicAlignments_1.14.1 gridExtra_2.3 knitr_1.17 [76] rtracklayer_1.38.0 bit_1.1-12 Hmisc_4.0-3 [79] ProtGenerics_1.10.0 stringi_1.1.6 Rcpp_0.12.13 [82] rpart_4.1-11 acepack_1.4.1
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In 99% of cases, this is an issue with the rtracklayer connection to UCSC. Gviz does not implement any of that functionality. I'd advise to test whether the rtracklayer UCSC functionality works for you, and if not, to reach out to the rtracklayer package maintainers.
Florian
Thanks for the pointer.. I'll check the rtracklayer connection (as much as I can do)..