Genomic selection

Step 1:Data input

Users can upload PED, MAP, and phenotype files for the GS analysis. Please note that the input files for the reference and candidate population should be prepared separately and have an identical set of genetic markers. Please --download the example datasets-- and check the tutorial for detailed information about the file formats. The PED, MAP, and phenotype files for the reference population should be named as “mydata.ref.ped”, “mydata.ref.map”, and “mydata.ref.phe”. The PED and MAP files for the candidates should be named as “mydata.predict.ped” and “mydata.predict.map”. Please note, users can upload a file with a maximum size of 50MB. Datasets larger than that should be uploaded via FTP or analyzed locally with the standalone package.

Reference dataset:



Please upload the .ref.ped file:

or select an uploaded file

or use an example dataset




Please upload the .ref.map file:

or select an uploaded file

or use an example dataset




Please upload the .ref.phe file:

or select an uploaded file

or use an example dataset



Prediction dataset:



Please upload the .predict.ped file:

or select an uploaded file

or use an example dataset




Please upload the .predict.map file:

or select an uploaded file

or use an example dataset




Step 2: Model selection

Users can predict Genomic Estimated Breeding Values (GEBV) with one of three GS models: Genomic Best Linear Unbiased Prediction (GBLUP), Bayesian Lasso, and Sparse Neural Networks (SNN).

High levels of linkage disequilibrium (LD) and low quality SNPs affect both performance and efficiency of GS models. High LD and low quality SNPs were pruned by default. Please note, analysis of large dataset could be very slow when turning off this setting.

LD pruning and quality control 

Step 3: Cross-validation

Users can select this setting to conduct 10-fold Cross-validation (CV) on reference dataset. Please note, the analysis time will be significantly increased when turning on this setting.

Cross-validation control


Step 4: Submit your job

Be notifled by email (Tick this box if you want to be notified by email when the results are available)




if available,the title will be included in the subject of the notification email and can be used as a way to identify your analysis.

Results

You may bookmark the following web address and view your results later. Please note that the results will be stored for 7 days.

Your job is currently running ... Please be patient. Analysis successful ! The analysis is failed. Please verify the formats of your input files. In case that you are using the example datasets from FigShare (Version 1) , please note that the error is caused by a wrong sample_information file. We have updated this file in the lastest version of the examples (https://figshare.com/articles/dataset/AMBP_case_study/19390652).



Sample phylogeny and genomic estimated breeding values.





Estimated marker effects.





Download all the results