Question: create null sequences with gkmSVM for mouse genome mm10
2
gravatar for fusion.slope
13 months ago by
fusion.slope210
fusion.slope210 wrote:

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

dna gkmsvm R • 374 views
ADD COMMENTlink modified 3 days ago • written 13 months ago by fusion.slope210
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1537 users visited in the last hour