How To Display Reads Profiling By Sense And Antise Separately Using Gbrowse?

Question

[Zhlingl]

hello, i am using Gbrose to visualise NGS data, and i want to show the expression number of sense mapping reads and antisense mapping reads separately (in differnet tracks or use different colors, whatever), how can i do that? In the Gbrowse NGS toturial, i find coverage is suppose to achieve my requirements, i can successfully see the total coverage of sense plus antisense reads, can anybody help me to get the right config on display them seperately? or tell me any other method to fix this problem?

many thanks and best wishes!

following is my config of coverage part, waitting for your reply!

[Coverage] feature = coverage glyph = wigglexyplot database = NGSsam height = 50 fgcolor = black bicolorpivot = 20 poscolor = blue negcolor = red key = Coverage category = Reads label = 0 # Labels on wiggle tracks are redundant.

Answer 1

[Vitis]

I don't know whether you can do it with 'coverage' and 'wiggle_xyplot', but it is definitely possible to show strand information with feature 'match' and glyph 'segments'. The look is a bit different as it shows you the reads instead of a coverage curve. Example track configuration:

[XXXXX] feature = match glyph = segments draw_target = 1 show_mismatch = 1 mismatch_color = red database = XXXXX bgcolor = sub { my $f = shift; my $strand = $f->query->strand; if ($strand==1) { return 'blue'; } else { return 'red'; } } stranded = 1 fgcolor = white height = 5 label density = 50 bump = fast key = XXXXX reads mapping category = NGS