Re: How are subtracks configured?

Hi Sujai,

You can try explicitly setting the min_score and max_score, although as you point out, that may not be the
best solution, particularly for RNASeq datasets with disparate read coverages. Converting the read
coverage to Reads Per Million mapped (RPM), log2, or even both has helped to tame my datasets.

Yes, for the subtrack track stanza you will need to specify the database. I don't believe it's done in the
metadata file, but in the track conf stanza.

Since you have multiple bigWig files, you may want to look into the BigWigSet database adaptor, which
combines a directory of bigWig files into a single database. Another metadata text file included in the
directory is used to assign metadata to each bigWig file. You can read more about the BigWigSet adaptor in
the Bio::DB::BigWigSet POD, also found here
http://search.cpan.org/~lds/Bio-BigFile-1.07/lib/Bio/DB/BigWigSet.pm

The subtracks won't be on the same graph and scale, unless you use the new transparency option introduced
recently in GBrowse.

Hope that helps,
Tim

On May 30, 2012, at 1:07 PM, Sujai wrote:

Dear Gbrowse team

I'm trying to get two quantitative tracks to display as subtracks so that their min and max scales will be the same.

I've been through http://gmod.org/wiki/Creating_and_Managing_Subtracks_with_GBrowse2 but I'm
definitely missing something basic in my understanding, so am hoping someone can help me figure it out:

I already have two bigwig tracks that display perfectly. In the Database section:

[female.coverage.bw:database]
db_adaptor    = Bio::DB::BigWig
db_args       = -bigwig /var/www/html/gbrowse2/databases/female.coverage.bw<http://female.coverage.bw/>

[intestine.coverage.bw:database]
db_adaptor    = Bio::DB::BigWig
db_args       = -bigwig /var/www/html/gbrowse2/databases/intestine.coverage.bw<http://intestine.coverage.bw/>

And in the Tracks section:

[female.coverage.bw<http://female.coverage.bw/>]
feature  = summary
database = female.coverage.bw<http://female.coverage.bw/>
glyph    = wiggle_whiskers
height   = 50
key      = female.coverage.bw<http://female.coverage.bw/>
category = Normalised RNA coverage

[intestine.coverage.bw<http://intestine.coverage.bw/>]
feature  = summary
database = intestine.coverage.bw<http://intestine.coverage.bw/>
height   = 50
glyph    = wiggle_whiskers
key      = intestine.coverage.bw<http://intestine.coverage.bw/>
category = Normalised RNA coverage

I tried writing a new Track section called supertrack:

[supertrack]
feature  = summary
glyph    = wiggle_whiskers
height   = 50
metadata = /var/www/gbrowse2/databases/metadata.txt

And, in metadata.txt, I put:

[intestine.coverage.bw<http://intestine.coverage.bw/>]
:selected = 1
factor = intestine

[female.coverage.bw<http://female.coverage.bw/>]
:selected = 1
factor = female

And nothing shows up. Do I need to define the BigWig database adaptor in the metadata.txt file? What am I
doing wrong? Any help much appreciated!

Actually - am I even thinking about this correctly? Is a subtrack the best way to get the two tracks to have the
same scale? Or is there a better way?

I could manually set the min and the max of each track, but even though this is normalised RNA data, the range
is too much to be displayed when set to the min/max of the whole data set?

Best wishes,

- Sujai

Blaxter Lab, University of Edinburgh
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