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Gaggle Genome Browser

Import from files

GGB can import track data from tab delimited text files in several formats. To get started, Select Tracks|Import Track from the menu. Use the file chooser to select a file.

Hit next, and the import wizard shows a preview the contents of the file. You will need to check the checkbox if your file has column headers and select the format of the file. Select a loader. Pick Data Segments if you data relates to intervals on the genome with start and end coordinates (microarray probes, for example)

Segment based data

Data tied to an interval (aka segment, range) on the genome is represented with a start and end coordinate, as shown in the example below:

sequence          strand            start             end               value
chr               +                 1                 101               0.000999999833333342
chr               +                 91                191               0.09087445682576
chr               +                 181               281               0.180013327439859
chr               +                 271               371               0.267695074058861
chr               +                 361               461               0.353209953805683
chr               +                 451               551               0.435865763580759
...

Example file: quantitative.segments.txt

Positional data

Select Data Points if the data refers to point positions on the genome.

sequence          strand            position          value
chr               +                 1                 0.000999999833333342
chr               +                 91                0.09087445682576
chr               +                 181               0.180013327439859
chr               +                 271               0.267695074058861
chr               +                 361               0.353209953805683
chr               +                 451               0.435865763580759
...

Example file: quantitative.positional.txt

GFF

GGB also supports a variant of GFF, with columns seqid, source, type, start, end, score, strand, phase, attributes. An example is shown here:

sequence  source    feature   start     end       score     strand    phase     attributes
chr       ignored   ignored   1         101       0.00999   +         ignored   ID=unique name;Name=common name
chr       ignored   ignored   91        191       0.78950   +         ignored   ID=unique name;Name=common name
chr       ignored   ignored   181       281       0.97152   +         ignored   ID=unique name;Name=common name
chr       ignored   ignored   271       371       0.41831   +         ignored   ID=unique name;Name=common name
chr       ignored   ignored   361       461       -0.45146  +         ignored   ID=unique name;Name=common name

Example file: example.gff

Gene data files

Sequence   Strand  Start   End     Name    Common Name        Gene Type
chr        +       944     1914    ss01    bert               gene
chr        -       2010    3210    ss02    ernie              gene
chr        +       3579    4682    ss03    big bird           gene
chr        -       4848    5566    ss04    elmo               rna
chr        +       5885    7890    ss05    oscar the grouch   repeat
chr        -       8086    8800    ss06    grover             pfam

Example file: sesame.txt

Track type

Next select the track type, which indicates to the program what types of renderers are appropriate. Although this is partially determined by the actual shape of the data, and hence the loader used in the previous step, the program is not yet very smart about the choices it displays. Select quantitative.segment for segment based data and quantitative.positional for positional data points.

More hints

Loading track data from files is currently quite fragile. Make sure your sequence names match the sequences defined in the genome, the coordinates are all integers and the values are all floating point numbers. Strand can be '+', '-', or '.' (for no strand).

Help

Please feel free to ask questions on the Gaggle mailing list.

Back to help on importing data.

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