1 Sep 2011 03:15
gbrowse_syn add NGS data(bam,coverage)
hi,
i want to add NGS-coverage in gbrowse_syn ,so i changed the .conf file ,but only show the main database(default database) data,not the RNA_SEQ database. please read bellows.
--------------------------------
.synconf
[super]
tracks = Genes mRNA CoverageXyplot
color = blue
[wild]
tracks = Genes mRNA CoverageXyplot
color = red
------------------------------
wild.conf
[GENERAL]
description = Wild Cucumber Genome
database = wild_2011_08_15
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor DBI::mysql
-dsn dbi:mysql:database=wild_2011_08_15;host=localhost
-user gbrowse
-pass gbrowse123
......
.....
[RNA_SEQ_fruit:database]
db_adaptor = Bio::DB::Sam
db_args = -fasta /home/tant/databases/wild_RNA_SEQ/wild_chr.fa
-bam /home/tant/databases/wild_RNA_SEQ/Hw_fruit_l1.bam
-split 1
........
........
[Genes]
.....
.........
[mRNA]
......
......
[CoverageXyplot]
feature = coverage
glyph = wiggle_xyplot
database = RNA_SEQ_fruit
height = 50
fgcolor = black
bicolor_pivot = 20
pos_color = blue
neg_color = red
key = Coverage_ff (xyplot)
category = Reads_ff
------------------------------------
super.conf
the same to wild.conf
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