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