Hi,

I have some BAM files I've read into R as a GRanges object using readBamGappedAlignments()

I have done the same in order to make an annotated genome, GRanges object using makeTranscriptDbFromUCSC(), followed by transcriptsBy().

I can use countOverlaps, I want to plot my reads in the bamfile against the genome, and visualise it, as well as zooming in on different genes something like:

DIFFERENT READS:
                 ------
                       ------
                            ------
                   ------
                               ------

GENE           :---------------------------->

But preferably with more detail :)

Is there a "canned" way to . I have heard of a way to do it using GenomeGraphs, but the examples are for array data.

Apologies if this isn't the best arena for proposing this question! I appreciate it is quite specific. Thanks for your time.

Cheers