BSgenome.Dmelanogaster.UCSC.dm6 annotation issue
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jbeira • 0
@jbeira-13858
Last seen 3.9 years ago

Hello,

I've been using the bioconductor package BSgenome.Dmelanogaster.UCSC.dm6 after the dm6 release. However, there seems to be some issue with the annotation, as I get error messages regarding "chrUn_DS484210v1" - could someone help me figure out how to fix this? Or perhaps the package needs some checking since "dm3" works fine.

 

Thanks!

 

JB

bsgenome BSgenome.Dmelanogaster.UCSC.dm6 • 654 views
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It would be really helpful if you could update your post to include the commands you're running that produce the error, and also the output of sessionInfo() so the anyone trying to help can make sure they're using the same version of the package.

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Hi,

I'll emphasize Mike's comment: we cannot do much to help if we don't know WHAT error you get exactly and HOW to reproduce it. FWIW, BSgenome.Dmelanogaster.UCSC.dm6 contains the chrUn_DS484210v1 scaffold and I can load it on my machine:

> library(BSgenome.Dmelanogaster.UCSC.dm6)
> BSgenome.Dmelanogaster.UCSC.dm6[["chrUn_DS484210v1"]]
  2617-letter "DNAString" instance
seq: TACTTTATTACAAGACACTTATTGTTATCTA...TGAGTTACAAACAAATATATTGAAAATATTT

See my session info below.

H.

> sessionInfo()
R version 3.4.0 Patched (2017-04-26 r72630)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

Matrix products: default
BLAS: /home/hpages/R/R-3.4.r72630/lib/libRblas.so
LAPACK: /home/hpages/R/R-3.4.r72630/lib/libRlapack.so

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] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] BSgenome.Dmelanogaster.UCSC.dm6_1.4.1 BSgenome_1.45.1                      
 [3] rtracklayer_1.37.3                    Biostrings_2.45.3                    
 [5] XVector_0.17.0                        GenomicRanges_1.29.12                
 [7] GenomeInfoDb_1.13.4                   IRanges_2.11.12                      
 [9] S4Vectors_0.15.5                      BiocGenerics_0.23.0                  

loaded via a namespace (and not attached):
 [1] zlibbioc_1.23.0            GenomicAlignments_1.13.5  
 [3] BiocParallel_1.11.6        lattice_0.20-35           
 [5] tools_3.4.0                SummarizedExperiment_1.7.5
 [7] grid_3.4.0                 Biobase_2.37.2            
 [9] matrixStats_0.52.2         Matrix_1.2-10             
[11] GenomeInfoDbData_0.99.1    bitops_1.0-6              
[13] RCurl_1.95-4.8             DelayedArray_0.3.19       
[15] compiler_3.4.0             Rsamtools_1.29.0          
[17] XML_3.98-1.9              

 

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