Hi Lukas,
Well, I'm basically back to the original error I had when I started this work back in December. At that point, I'd decided that my bam files must have had chromosome or scaffold names that didn't exist in the reference genome. So I went back to the original data set and redid all of the alignments to make sure the version of the reference genome I was using was the same. It seems that I something is still not matching up.

How can I compare the set of chromosome names between the bam file and the reference genome?

> budFall1_MEDIP = MEDIPS.createSet(file="FallBud_brep1_aln_sorted.bam", BSgenome=BSgenome, extend=300, uniq=TRUE, shift=0, window_size=1000)
Reading bam alignment FallBud_brep1_aln_sorted.bam
Total number of imported short reads: 21038273
Extending reads...
Creating GRange Object...
Extract unique regions...
Number of unique short reads: 17855868
Error in as.environment(pos) :
  no item called "paste("package:", BSgenome, sep = "")" on the search list
In addition: Warning message:
In ls(paste("package:", BSgenome, sep = "")) :
  āpaste("package:", BSgenome, sep = "")ā converted to character string

Thanks,
________________________________
From: Lukas Chavez [lukas.chavez.mailings@googlemail.com]
Sent: Friday, March 28, 2014 10:58 AM
To: Vining, Kelly
Cc: bioconductor@r-project.org
Subject: Re: [BioC] MEDIPS.createSet error

Dear Kelly,

this error typically occurs when the chromosome names in your bam file do not entirely match the chromosome names in your BSgenome object. I suppose that in your bam file there are reads matching to a chromosome with a name that cannot be found in the BSgenome object.

Lukas


On Fri, Mar 28, 2014 at 10:42 AM, Vining, Kelly <Kelly.Vining@oregonstate.edu<mailto:Kelly.Vining@oregonstate.edu>> wrote:
Hello,
I'm coming back to a MEDIPS project after a long pause, and am having trouble reading in my .bam files. I'm using a custom reference genome that Lukas Chavez kindly helped me to make into a BSgenome object.  I'm not sure how to address the error message below. I hope it doesn't mean there is something wrong with my reference genome...

> budFall1_MEDIP = MEDIPS.createSet(file="FallBud_brep1_aln_sorted.bam", BSgenome=BSgenome, extend=300, uniq=TRUE, shift=0, window_size=1000)
Reading bam alignment FallBud_brep1_aln_sorted.bam
Total number of imported short reads: 21038273
Extending reads...
Creating GRange Object...
Extract unique regions...
Number of unique short reads: 17855868
Calculating genomic coordinates...Error in vector(length = supersize_chr[length(chromosomes)], mode = "character") :
  vector size cannot be NA/NaN

Thanks for help,
Kelly V.
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