The Consensus And Splitting Tool will allow you to select a dataset from GOBii, apply some basic filtering, carry out consensus calling of replicate samples, split the file by sample metadata, and create a project file for analysis in Flapjack. Details of these steps are provided below. Note: currently the pipeline is for 2 letter nucleotide datatypes only.
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Login
BrAPI URL
First, select enter the url URL for the environment that you would like to pull data from. The environment
For GOBii-GDM versions 2.2 and earlier, the URL will look something like http://apigdm.gobii.orgorg:8081/gobii-dev/This url -my_crop/, where the crop/environment name is my_crop.
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For GOBii-GDM versions 2.2 and earlier this URL can be copy / pasted from the Extractor link in the main portal. |
For GOBii-GDM versions 3.0 and later, the URL will look like http://gdm.gobii.org/gdm/crops/my_crop/.
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This URL automatically points to /brapi/v2 and so you don’t need to add this extension to the |
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URL as you would for import of data into some other tools |
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(e.g. Flapjack). |
Credentials
Log in to the GOBii-GDM system using your GOBii-GDM credentials.
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Table 1. Example metadata used in CAST
Germplasm_name | dnarun_name | dnasample_num | germplasm_par1 | germplasm_par2 | germplasm_pedigree | dnasample_group |
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cross1_p1/p2 | cross1_p1/p2-sample1 | 1 | p1 | p2 | p1/p2 | cross1 |
cross1_p1/p2 | cross1_p1/p2-sample2 | 2 | p1 | p2 | p1/p2 | cross1 |
cross1_p1/p2 | cross1_p1/p2-sample3 | 3 | p1 | p2 | p1/p2 | cross1 |
cross2_p3/p4 | cross2_p3/p4-sample1 | 4 | p3 | p4 | p3/p4 | cross2 |
cross2_p3/p4 | cross2_p3/p4-sample2 | 5 | p3 | p4 | p3/p4 | cross2 |
cross2_p3/p4 | cross2_p3/p4-sample3 | 6 | p3 | p4 | p3/p4 | cross2 |
p1 | p1-sample1 | 7 | ||||
p2 | p2-sample2 | 8 | ||||
p3 | p3-sample3 | 9 | ||||
p4 | p4-sample1 | 10 | ||||
p4 | p4-sample2 | 11 |
Filter Data
Use this page to filter your data based on marker and sample percent data.
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