Category Archives: GBrowse

Integrate bigWig files into GBrowse

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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): 

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

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:

[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

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.