谭涛 | 1 Sep 2011 03:15
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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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