smoothing of wiggle_xyplot with BAM database

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smoothing of wiggle_xyplot with BAM database

Matthew Hobbs
Hi,

I have some tracks which show coverage of some NGS data stored in BAM format (see configuration excerpts below). I would like to see what the coverage looks like with some smoothing but can't make this happen. The wiggle_xyplot's "smoothing" and "smoothing_window" options don't seem to have any effect on what is produced - should they?  I see in the Bio::DB::Sam documentation that it is possible to calculate  coverage across larger bins by using e.g. "coverage:500" but how do I do this from within the gbrowse configuration file, where "coverage:500" is used for semantic zooming?

I am using Bio-SamTools-1.14, Bio-Graphics-2.02, Generic-Genome-Browser-2.03

Thanks for any help,

Matthew


[42563_LIB4_2:overview]
database      = 42563_LIB4
feature      = coverage:100001
glyph        = wiggle_xyplot
height       = 50
min_score    = 0
max_score    = 10
autoscale    = local

[42563_LIB4:database]
db_adaptor    = Bio::DB::Sam
db_args       = -bam   /var/www/html/gbrowse2/databases/bamtest/42563_LIB4.bam
-fasta /var/www/html/gbrowse2/databases/bamtest/UMD3.fa
-expand_flags 1
search options= default


MATTHEW HOBBS| Senior Research Fellow
Faculty of Veterinary Science


THE UNIVERSITY OF SYDNEY
T +61 2 9351 1673 | F +61 2 9351 1693



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