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


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:

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)

 [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           

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
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1563 users visited in the last hour