Hello,

Can one convert a BSgenome file to GRanges format? Also, can one convert a bam file to GRanges format?

If so, how to do?

Thanks,
Philip Terry
Univ. Nebraska-Lincoln

Your first question doesn't really make sense. A BSgenome package contains the genome for a given species, where a GRanges object contains (at its most basic) the chromosome and location of regions of interest on the genome (where region of interest is usually something like transcripts, genes, SNPs, etc).

To convert bam to GRanges you want the Rsamtools package. See the overview vignette here:http://bioconductor.org/packages/release/bioc/vignettes/Rsamtools/inst/doc/Rsamtools-Overview.pdf