Hi!

I have basically two questions. I'm trying to analyze RNA-seq data, contained in BAM files, using applyPileups. The ApplyPileupsParam, however, needs the 'which' paremeter, which needs a GRanges object.

Is there an easy way to, say, get all chromosomes from a file (not contigs)?

And since it seems to require an IRanges object for the 'ranges' parameter of the GRanges object, is there an easy way to simply get all the data from each chromosome? Or do I have to find then plug in the coordinates for each chromosome?

Thank you!

as(seqinfo(BamFile("your.bam")), "GRanges") (or BamFileList()) to query the seqinfo in the header of the bam file. GenomeInfoDb::keepStandardChromosomes() will trim to just the 'standard' chromosomes.

I'm surprised it requires a which argument. You could just coerce the Seqinfo to a GRanges, e.g. for hg19:

as(Seqinfo(genome="hg19"), "GRanges")