##gff-version 3

#Quantitative Data

#GBrowse can plot quantitative data such as alignment scores,
#confidence scores from gene prediction programs, and microarray
#intensity data. There is a simple format that can be placed directly
#inside of a GFF3 file but does not scale to very large data sets, and
#a "WIG" format designed for very high-density quantitative data such
#as tiling arrays.

#We first look at the simple format: 

ctg123	affy	microarray_oligo			1	100	281	.	.	Name=Expt1
ctg123	affy	microarray_oligo	101	200	183	.	.	Name=Expt1
ctg123	affy	microarray_oligo	201	300	213	.	.	Name=Expt1
ctg123	affy	microarray_oligo	301	400	191	.	.	Name=Expt1
ctg123	affy	microarray_oligo	401	500	288	.	.	Name=Expt1
ctg123	affy	microarray_oligo	501	600	184	.	.	Name=Expt1

#In this format, which can be embedded directly in the GFF3 file, each
#data point is a distinct feature with a start and end point. The
#features are grouped together by giving them a common experimental
#name so that they can be retrieved together. We use the score field
#(column 6) to represent the quantitative information
#(e.g. hybridization intensity).

#In contrast, when using WIG format, the quantitative data is kept
#outside of the main database in a special-purpose binary file that is
#kept somewhere on the file system. In this case the GFF3 file
#contains a single line per experiment like this one:

#ctg123 . microarray_oligo 1 50000 . . . Name=example;wigfile=/usr/data/ctg123.Expt1.wig

#The .wig file is created and managed using a script called
#wiggle2gff3.pl that comes with GBrowse. Instructions on how to use
#this script is described in the GBrowse Administration Tutorial.