Question: Warning in "countReads" [Warning message: In .Seqinfo.mergexy(x, y) : The 2 combined objects have no sequence levels in common.]
gravatar for kyliecode
2.1 years 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!


greylistchip • 1.4k views
ADD COMMENTlink modified 2.1 years ago • written 2.1 years 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 2.1 years ago by k.vitting.seerup100

Yes, I've gotten this error too,  I tried to add "Chr" to the beginning of each chromosome in the bam file, but I then received another error 

Error in mergeNamedAtomicVectors(seqlengths(x), seqlengths(y), what = c("sequence",  : 

  sequence chrM has incompatible seqlengths:

  - in 'x': 16569

  - in 'y': 16571

In the case that you want to use GreyListChIP, but aligned fastq files using ensembl already, I'm still not so clear how to remedy the problem (sans, of course, going back and re aligning using UCSC). Any suggestions?


ADD REPLYlink written 10 months ago by Yonatan Amzaleg0

The genomes have to match exactly.  In particular, UCSC and Ensembl genomes differ, in addition to chromosome naming, in tiny ways that almost never matter, until a situation like this.  As you've already found, just changing the chromosme names isn't enough (though you can get away with it sometimes).  You have to align to the exact genome you're using to generate the grey list (or many other analyses).

ADD REPLYlink written 10 months ago by Gord Brown590
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