You can run this analysis as a Batch Analysis across multiple data sets (or views) at once.
This analysis translates trait marker genotyping data into presence or absence of QTLs.
In addition to this help page, you can also read the tutorial, which runs through the process of running the analysis and viewing the results with a sample dataset.
Forward Breeding analysis requires additional input parameters that can be provided via a GOBii QTL Format formatted file.
The QTL file is a tab-delimited file that contains the association between QTL and markers including their favourable and unfavourable alleles.
This is how the file looks like:
# fjFile = qtl-gobii marker_group_name marker_name germplasm_group platform fav_allele unfav_allele rust_1 m1 rust SNPChief A T rust_1 m2 rust SNPChief A T sub_1 m3 submergence SNPChief A T sub_1 m4 submergence SNPChief T A dwarf-allele1 m5 height Casper AAT A waxy m6 grain quality Casper + -
# fjFile = qtl-gobii line is only required for importing the QTL file by dragging and dropping it into the Flapjack application. The line containing the column names is required. The column names does not need to match exactly as showed above, although they need to follow the exact arrangement. The first 5 columns (until
fav_allele) are required to be in the file.
QTL File Headers
||Defines the grouping of markers, or to which QTL markers are associated|
||Marker name that matches with the dataset|
||Optional. Any free text, this column is not used in the analysis|
||The allele of a marker that indicates the desirable status of the QTL|
||Optional. The allele that indicates the undersirable status of the QTL|
A map file is optional for this analysis. It follows the standard Flapjack Map file format.
This analysis outputs the following statistics for each marker group.
- Partial Match (0.0 - 1.0)
- Calculated by averaging matching scores of favourable alleles for each marker, 0.5 for het, 1.0 for homozygous.
- Complete Match (0.0, 0.6, 1.0)
- Calculated by taking the maximum matching scores for favourable alleles at each marker, 0.6 for het, 1.0 for homozygous.
|Samples||Marker Group||Markers||Marker Scores||Partial Match||Complete Match|