GBrowse visualization

cascoamarillo · 02-10-2012, 02:29 PM

Hi,

In the GenomeBrowser 2.0, when I load my custom track (is this case is a BAM file) I can see the coverage and reads (when I zoom in); but I'm not able to diferenciate the reads that match the positive/negative strand (i.e. with different colors). I've tried to modify the config file without successful. This is what I got:

Code:

[mapping_sorted.bam]
feature   = coverage:2000
min_score    = 0
glyph        = wiggle_xyplot
height       = 200
fgcolor      = black
bgcolor      = black
autoscale    = local


[mapping_sorted.bam]
database = database_0 # do not change this!
feature      = read_pair
glyph        = segments
draw_target  = 1
show_mismatch = 1
mismatch_color = red
bgcolor      = blue
fgcolor      = blue
height       = 3
label        = 1
label density = 50
bump         = fast
key          = Shared track from http://mapping_sorted.bam

Any help?
Thanks

ffinkernagel · 02-10-2012, 03:06 PM

you need a callback for the bgcolor.
here's what I'm using
bgcolor = sub { my $f = shift; return 'purple' unless $f->type eq 'match'; return $f->reversed ? 'blue' : 'yellow'; }
which covers slightly more than just the forward/reversed case.

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02-10-2012, 02:29 PM	#1
cascoamarillo Senior Member Location: MA Join Date: Oct 2010 Posts: 160	GBrowse visualization Hi, In the GenomeBrowser 2.0, when I load my custom track (is this case is a BAM file) I can see the coverage and reads (when I zoom in); but I'm not able to diferenciate the reads that match the positive/negative strand (i.e. with different colors). I've tried to modify the config file without successful. This is what I got: Code: [mapping_sorted.bam] feature = coverage:2000 min_score = 0 glyph = wiggle_xyplot height = 200 fgcolor = black bgcolor = black autoscale = local [mapping_sorted.bam] database = database_0 # do not change this! feature = read_pair glyph = segments draw_target = 1 show_mismatch = 1 mismatch_color = red bgcolor = blue fgcolor = blue height = 3 label = 1 label density = 50 bump = fast key = Shared track from http://mapping_sorted.bam Any help? Thanks

02-10-2012, 03:06 PM	#2
ffinkernagel Senior Member Location: Marburg, Germany Join Date: Oct 2009 Posts: 110	you need a callback for the bgcolor. here's what I'm using bgcolor = sub { my $f = shift; return 'purple' unless $f->type eq 'match'; return $f->reversed ? 'blue' : 'yellow'; } which covers slightly more than just the forward/reversed case.