/usr/share/EMBOSS/test/data/gmod-quantitative.gff3 is in emboss-test 6.6.0-1.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 | ##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.
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