Quick or Full analysis: which one do I need?
The difference between Quick and Full analysis, and which one your data needs.
Use Quick for any population: a germplasm collection, a diversity panel, several families or a breeding population. Use Full only for one biparental cross (an F1 full-sib family) with both parents genotyped. Full does everything Quick does and adds a linkage map and QTL mapping.
Both are under New Analysis → End-to-End Gene Discovery: Start Quick analysis or Start Full analysis. Each card lists the files it needs.
What each one runs
| Quick | Full | |
|---|---|---|
| Population | Any | One F1 cross, both parents genotyped |
| BLUPs from your field data | Yes | Yes |
| Genotype quality control | Yes | Yes, plus a check of every offspring against the two parents |
| Genomic heritability | Yes | Yes |
| GWAS | Yes | Yes |
| Linkage map | No | Yes |
| QTL interval mapping with a genome-wide permutation threshold | No | Yes |
| Which parent a QTL comes from, and a marker for selection | No | Yes, for a significant QTL |
| Candidate-gene search region | Each region of significant GWAS markers, ±250 kb | The QTL’s LOD-support interval, bounded by recombination in your cross |
| Run time | Shorter | Longer, because it builds a linkage map and runs the permutation test |
Why Full needs a biparental cross
QTL mapping uses the recombination between markers in one family to narrow a signal to a region. That requires a linkage map built from the offspring of two known parents. In a diversity panel or a mix of families, there is no single map to build, so Quick’s GWAS is the right analysis there.
In a biparental cross, the QTL scan covers every chromosome. If the QTL chromosome differs from the GWAS top hit, the results say so; in a biparental cross the QTL chromosome is the one to trust. One QTL is characterized per trait; other chromosomes whose peak also clears the threshold are listed with their position and LOD.
Choosing the parents
When you upload a genotype file, CacaoIQ checks whether it is one biparental family and, if so, which two samples are its parents. The run panel then fills in the Parents setting, with the note “Looks like one biparental cross”. Genotypes can’t tell which parent is the female, so the order comes from sample names only when they say so (for example _MOM and _DAD). Check which sample is set as the Female (seed) parent and which as the Male (pollen) parent.
If no cross is detected, Full stays unavailable until you choose the parents yourself: click Add the parents of a biparental cross and pick both. On GBS or DArTseq data, detection often misses a real cross; see Known issue: parent detection on GBS data.
Candidate genes in each mode
Candidate genes appear only for a significant locus: a marker above the Bonferroni threshold in GWAS, or a QTL above the genome-wide permutation threshold in Full. The app labels which kind of search region produced each gene list.
Other workflows
- Phenotype data only, no genotypes: use Phenotypic Modeling (BLUPs, repeatability or broad-sense H²).
- A factorial mating design with several female and male parents: use the GCA/SCA analysis in Phenotypic Modeling.
Related articles
- Which heritability does CacaoIQ report?
- Which genotype file formats work
- Where are my results saved?
Still stuck? Write to support@scilytics.ai with your system and what you see on screen. Don’t attach data files. The first reply comes within 2 business days.