[Bioperl-l] How to plot coverage using Bio::DB::Sam and Bio::Graphics?

[Michael Morley]

Have a few questions some perhaps too simple which I know I should have 
been able to find the answers but have eluded me.

Problem:
What I want to do visualize coverage (Illumina RNA-seq) across a gene 
for 40 or so samples. I thought about gbrowse but what I was hoping to 
was to use Bio::Graphics and created a few PNGs of the genes I'm 
interested in, nothing too fancy.


My current attempt:

So I've used Bio::DB::Sam (thank you LDS!!,great package) as following.. 
Works perfect.

my $features = 
$sam->features(-type=>'coverage',-seq_id=>$chrom,-start=>$genomest,-end=>$genomest);
 
Then I tried this:

$panel->add_track($features,
                     -glyph => 'xyplot',
                    -graph_type=>'histogram',
                );


After poking at the return of '-type=converge', I don't think this is 
possible directly but any ideas how I can do it?

The coverage is too deep in the region to plot every sequence in the 
alignment,  I was able to do it just was not useful.


One last question.. I also would like to plot the gene model as well. If 
I simply grab the genbank file for refseq NM###, the features only have 
exon,cds,etc and coordinates based off the mRNA seq. So how does one get 
the genomic info and then create the track for a gene/transcript as you 
would see in gbrowse?



Any help I'd greatly appreciate it!


-Michael