Question: Warning in "countReads" [Warning message: In .Seqinfo.mergexy(x, y) : The 2 combined objects have no sequence levels in common.]
gravatar for kyliecode
12 months ago by
kyliecode0 wrote:

Dear developer & users,

Hi, I've been trying GreyListChIP but was not succeed when using own bam file (The package installation is alright, which tested by the sample data)

Here's the code:

path <- system.file("extra", package="GreyListChIP")
fn <- file.path(path,"T1-D0-I.dup.removed.sort.bam")
gl <- new("GreyList",BSgenome.Mmusculus.UCSC.mm10)
gl <- countReads(gl,fn)
gl <- calcThreshold(gl,reps=100,sampleSize=30000,p=0.99,cores=4)

Warning generated by countReads:

In .Seqinfo.mergexy(x, y) :
  The 2 combined objects have no sequence levels in common. (Use
  suppressWarnings() to suppress this warning.)

Warning generated by calcThreshold:

Error in stuff[[x]] : subscript out of bounds

when I inspect the gl, only the tiles and file path return. I think the I was stuck since the countReads step.

GreyList on Mus musculus (UCSC mm10)
  tiles: 5333798
  files: /Library/Frameworks/R.framework/Versions/3.4/Resources/library/GreyListChIP/extra/T1-D0-I.dup.removed.sort.bam


Any help will be appreciated. Thanks a lot!


ADD COMMENTlink modified 12 months ago • written 12 months ago by kyliecode0

That is usually the error one get when there are differences in the chromosome names of the features compared - fx one being UCSC ("chr1") while the other is Ensembl (1).

ADD REPLYlink written 12 months ago by k.vitting.seerup20
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