Question: MEDIPS.createSet error
4.2 years ago by
Vining, Kelly • 220
Vining, Kelly • 220 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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