Integrate bigWig files into GBrowse

Lately, I have waisted quite a lot of time trying to integrate bigWig files into GBrowse.

At first, I had problems with installation of Bio::DB::BigWig in Ubuntu 14.04 x64. I had to combine tips from several places (this was the most helpful):

[code lang=”bash”]wget http://hgdownload.soe.ucsc.edu/admin/exe/userApps.v310.src.tgz
tar xfz userApps.src.tgz
cd userApps/kent/src/

# in inc/common.mk replace `CFLAGS=` line with `CFLAGS=-fPIC`

cd lib/
make
cd ..

sudo -i
export MACHTYPE=x86_64
export KENT_SRC=`pwd`
cpan Bio::DB::BigWig
[/code]

Then, I have spent quite a lot of time trying to incorporate multiple bigWig files at once. This can accomplished with Bio::DB::BigWigSet. Just add this to your genome.conf:

[code lang=”bash”]
[RibosomalRNASeq:database]
db_adaptor = Bio::DB::BigWigSet
db_args = -dir /path/to/your/bigWig/files
-feature_type summary
[All]
database = RibosomalRNASeq
feature = summary
glyph = wiggle_density
height = 15
category = Ribosomal RNA-Seq
[/code]

Note, your bigWig files should be placed in one directory and end with .bw.
Additionally, you can create meta.bw file that will define additional information about your samples.