Question: Gviz unable to retrieve cytoband data for sacCer3 when trying to create ideogram
0
gravatar for bertb
9 weeks ago by
bertb0
bertb0 wrote:

Hello,

I'm trying to create an ideogram track in Gviz, but I receive the following error message that seems to have an issue with my chosen genome:

'''

ideogram <- IdeogramTrack("chrIX", "sacCer3")

Warning message: In value[3L] : There doesn't seem to be any cytoband data available for genome 'sacCer3' at UCSC or the service is temporarily down. Trying to fetch the chromosome length data. '''

Is anybody familiar with this error, or a possible workaround?

Thank you,

B

'''

sessionInfo() R version 3.6.0 (2019-04-26) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 17134)

Matrix products: default

locale: [1] LCCOLLATE=EnglishUnited States.1252 LCCTYPE=EnglishUnited States.1252
[3] LCMONETARY=EnglishUnited States.1252 LCNUMERIC=C
[5] LC
TIME=English_United States.1252

attached base packages: [1] grid stats4 parallel stats graphics grDevices utils datasets [9] methods base

other attached packages: [1] Gviz1.28.0 rtracklayer1.44.0
[3] GenomicAlignments1.20.0 Rsamtools2.0.0
[5] Biostrings2.52.0 XVector0.24.0
[7] SummarizedExperiment1.14.0 DelayedArray0.10.0
[9] BiocParallel1.17.18 matrixStats0.54.0
[11] Biobase2.44.0 GenomicRanges1.36.0
[13] GenomeInfoDb1.20.0 IRanges2.18.0
[15] S4Vectors0.22.0 BiocGenerics0.30.0

loaded via a namespace (and not attached): [1] httr1.4.0 bit640.9-7 splines3.6.0
[4] Formula
1.2-3 assertthat0.2.1 BiocManager1.30.4
[7] latticeExtra0.6-28 blob1.1.1 BSgenome1.52.0
[10] GenomeInfoDbData
1.2.1 progress1.2.0 pillar1.3.1
[13] RSQLite2.1.1 backports1.1.4 lattice0.20-38
[16] biovizBase
1.32.0 glue1.3.1 digest0.6.18
[19] RColorBrewer1.1-2 checkmate1.9.3 colorspace1.4-1
[22] htmltools
0.3.6 Matrix1.2-17 plyr1.8.4
[25] XML3.98-1.19 pkgconfig2.0.2 biomaRt2.40.0
[28] zlibbioc
1.30.0 purrr0.3.2 scales1.0.0
[31] tibble2.1.1 htmlTable1.13.1 AnnotationFilter1.8.0
[34] ggplot2
3.1.1 GenomicFeatures1.36.0 nnet7.3-12
[37] lazyeval0.2.2 survival2.44-1.1 magrittr1.5
[40] crayon
1.3.4 memoise1.1.0 foreign0.8-71
[43] data.table1.12.2 tools3.6.0 prettyunits1.0.2
[46] hms
0.4.2 stringr1.4.0 munsell0.5.0
[49] cluster2.0.9 ensembldb2.8.0 AnnotationDbi1.46.0
[52] compiler
3.6.0 rlang0.3.4 RCurl1.95-4.12
[55] dichromat2.0-0 rstudioapi0.10 VariantAnnotation1.30.0 [58] htmlwidgets1.3 bitops1.0-6 base64enc0.1-3
[61] gtable0.3.0 curl3.3 DBI1.0.0
[64] R6
2.4.0 gridExtra2.3 knitr1.22
[67] dplyr0.8.0.1 bit1.1-14 Hmisc4.2-0
[70] ProtGenerics
1.16.0 stringi1.4.3 Rcpp1.0.1
[73] rpart4.1-15 acepack1.4.1 xfun0.6
[76] tidyselect
0.2.5

'''

ADD COMMENTlink modified 9 weeks ago by Robert Ivanek610 • written 9 weeks ago by bertb0
Answer: Gviz unable to retrieve cytoband data for sacCer3 when trying to create ideogram
0
gravatar for Robert Ivanek
9 weeks ago by
Robert Ivanek610
Switzerland
Robert Ivanek610 wrote:

Hi,

This was just a warning not error, telling you that there is no cytoband data available for yeast genome ''sacCer3". However in that case, Gviz draws a simple chromosome highlighting the position of your interest:

library(Gviz)
plotTracks(ideogram, from=1e5, to=1.5e5)

Best Robert

ADD COMMENTlink written 9 weeks ago by Robert Ivanek610

Thanks for your response, Robert. You're right, I'm able to continue to plot a track, but I was hoping to include an ideogram that represented sacCer3. Perhaps there is simply no data available for sacCer3.

ADD REPLYlink written 9 weeks ago by bertb0

There is no cytoband data for sacCer3 at UCSC.

ADD REPLYlink written 9 weeks ago by Robert Ivanek610

Ok. Thanks Robert. Ben

ADD REPLYlink written 9 weeks ago by bertb0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 169 users visited in the last hour