Question: Error creating custom genome: BSgenomeForge function (MEDIPS package in R)
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gravatar for lakhujanivijay
3.8 years ago by
lakhujanivijay5.1k
India
lakhujanivijay5.1k wrote:

Hi,

I am using the MEDIPS package for MeDIP-seq analysis where I am trying to create a custom genome for Vigna radiata (not already present in the package) and I am referring to below manual for guidance:

https://www.bioconductor.org/packages/devel/bioc/vignettes/BSgenome/inst/doc/BSgenomeForge.pdf

I have:

  1. Genome file (gzipped) of V.radiata.

  2. Seed file called BSgenome.Vradiata.UCSC.vr1-seed created referring to the manual (above link) section 2.2 Prepare the BSgenome data package seed file at page#4.

Now, I ran following commands:

> library(BSgenome)
> forgeBSgenomeDataPkg("path/to/my/seed")

where path/to/my/seed = my actual path to seed file.

I encountered following error:

Creating package in ./BSgenome.Vradiata.UCSC.vr1
Error in fetchSequenceInfo(genome) : genome "vr1" is not supported

Here is the session information:

> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS release 6.6 (Final)

locale:
 [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C             
 [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8    
 [5] LC_MONETARY=en_US.utf8    LC_MESSAGES=en_US.utf8   
 [7] LC_PAPER=en_US.utf8       LC_NAME=C                
 [9] LC_ADDRESS=C              LC_TELEPHONE=C           
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C      

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

other attached packages:
 [1] MEDIPS_1.22.0        Rsamtools_1.24.0     BSgenome_1.40.1     
 [4] rtracklayer_1.32.2   Biostrings_2.40.2    XVector_0.12.1      
 [7] GenomicRanges_1.24.3 GenomeInfoDb_1.8.7   IRanges_2.6.1       
[10] S4Vectors_0.10.3     BiocGenerics_0.18.0

loaded via a namespace (and not attached):
 [1] DNAcopy_1.46.0             AnnotationDbi_1.34.4      
 [3] zlibbioc_1.18.0            GenomicAlignments_1.8.4   
 [5] BiocParallel_1.6.6         tools_3.3.1               
 [7] SummarizedExperiment_1.2.3 Biobase_2.32.0            
 [9] DBI_0.5-1                  gtools_3.5.0              
[11] preprocessCore_1.34.0      bitops_1.0-6              
[13] RCurl_1.95-4.8             biomaRt_2.28.0            
[15] RSQLite_1.0.0              XML_3.98-1.4

I am clueless. Please help.

PS: I can provide the seed file if required; please let me know.

bsgenomeforge medips medip-seq • 1.1k views
ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by lakhujanivijay5.1k
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