[Gmod-gbrowse] bam vs bigWig coverage and scaling

[Gregor R. <gre...@fr...>]

Hi all,

i have 3 simple questions:

a) i converted my bam to bigWig (each aligned read contributes +1 at 
each position spanning the read). I am now comparing the bigWig track 
with the coverage bam track, the database definitions are:

[bigwig_db:database]
db_adaptor    = Bio::DB::BigWigSet
db_args       = -dir /big_wig_folder

[bam_db:database]
db_adaptor     = Bio::DB::Sam
db_args        = -bam   /path_to_bam_file

and i am using:

glypx = wiggle_xyplot

For feature i am using "coverage" for the bam track and "summary" for 
the bigWig track. What is the difference?

If you look at figure bam_vs_bigwig_coverage.png, you will see that 
coverage at centre is 27 for bigWig (bottom) and 35 for the bam track 
(top). I checked the sam file and the correct coverage is 27 (bigWig), i 
don't know how the bam coverage is computed?

b) if i zoom out to chr1 (scaling is set to local min/max), you see the 
result in figure scaling_1.png. The selected region has the highest peak 
(8500), but you can see other higher regions in the bam coverage track. 
Why? Also the y-axis on this track now shows only 347, but the bigWig 
track correctly shows 8554.

c) If you look at figure whiskers.png, i am using the whiskers glyph for 
the bigWig track. What is the difference between xyplot and whiskers? I 
don't understand why the tops of the values are being cut off (yellow 
color), and at value 8000.

---
To sum up, i would like to show the bigWig for coverage (it looks very 
nice, the combined forward/reverse strand with red/blue colors). The 
problem is i would need some kind of log-value scaling or something like 
that (because if a user zooms out to the entire chromosome it's very 
difficult to see where the peak regions are).

Any help appreciated,

Thanks,
Gregor

-- 
Gregor Rot
Bioinformatics Laboratory
Faculty of computer and information science
SI-1000 Ljubljana
Slovenia
http://www.fri.uni-lj.si/en/gregor-rot