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> 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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