Hello,  

does anybody of you has ever tried to generate null model of DNA sequences in mouse using the gkmSVM package? It works perfectly for human but for mouse it does not. I am wondering if any of you have ever used this package for mice and had the same problem.   

The error problem when I use the genNullseqs function is:  

    library(gkmSVM)
    library(BSgenome.Mmusculus.UCSC.mm10)
    library(BSgenome.Mmusculus.UCSC.mm10.masked)
    library(IRanges)
    
    genome=BSgenome.Mmusculus.UCSC.mm10.masked
    
    fileBedBreaks="Rep1.intersec.Rep2.cov.major2.sort.uniq.bed"
    fileFastaPos="Rep1.intersec.Rep2.cov.major2.all.sort.uniq.bed.pos.fa"
    fileBedNeg="Rep1.intersec.Rep2.cov.major2.all.sort.uniq.Random.gkmSVM.bed"
    fileFastaNeg="Rep1.intersec.Rep2.cov.major2.all.sort.uniq.Random.gkmSVM.fa"
    genNullSeqs(inputBedFN=fileBedBreaks,nMaxTrials=5,xfold=2,genome=genome,
                outputPosFastaFN=fileFastaPos,outputBedFN=fileBedNeg,outputNegFastaFN=fileFastaNeg)

 
`Error in normalizeDoubleBracketSubscript(i, x, exact = exact) : subscript "TRF" matches no name`  

TRF is related with the tandem repeats because it means Tandem Repeats Finder. But what does it means the problem??

Thanks in advance for any reply

I hit this same problem and figured out that it's because the BSgenome.Mmusculus.UCSC.mm10.masked on Bioconductor (as of May 2020) only has two masks included (AGAPS and AMB), whereas previous genomes included the TRF mask as well, which is what gkmSVM is looking for. 

Thankfully, on GitHub, Zhang (Frank) Cheng has added the TRF mask to the mm10 genome at [https://github.com/biomystery/BSgenome.Mmusculus.UCSC.mm10.masked][1]

I had to uninstall the Bioconductor version of mm10 and reinstalled using `remotes::install_github("biomystery/BSgenome.Mmusculus.UCSC.mm10.masked")`


  [1]: https://github.com/biomystery/BSgenome.Mmusculus.UCSC.mm10.masked