LoadExperiment

LoadExperiment enables you to load a set of quantitative experimental data for a genome in CoGe. The data can then be viewed alongside annotation in GenomeView.

Input

• Name: Name of experiment
• Description: Description of experiment
• Version: Version of experiment
• Source: Where is the data from? This could be you, your lab, your university, a sequencing center, your collaborator.
• Restricted: Is this experiment public or restricted to you and your collaborators
• Genome: Select the appropriate genome from CoGe
• Select Data File: Opens a window for specifying the input data file

Data File

You can select and retrieve data file located at:

• The iPlant Data Store
• An FTP server
• Your computer (Upload)

Data File Name Extension

Note: file types are detected through the file extension name.

• Quantitative data (numbers): Data is expected to be comma delimited and the file name must end with '.csv'. E.g. 'my_experiment.csv'

Data Format

The data format is very important! Here is an example set of data:

#CHR,START,STOP,STRAND,VALUE1(0-1),VALUE2(ANY-ANY)
Chr1,11486,12316,1,0.181430277220112,7.3980806218146
Chr1,27309,28272,1,0.944373742485446,5.08225285439412
Chr1,32484,32978,1,0.328500324191726,1.97719838086201
Chr1,41942,42508,-1,0.825027233105203,6.56057592312617
Chr1,56394,57527,-1,0.183234367788511,0.795527328556531
Chr1,67705,68809,-1,0.956523086778851,5.20992343466606
Chr1,71144,72409,1,0.42955128220331,1.80604269639474
Chr1,81671,82833,1,0.626003507696723,2.77834108023821
Chr1,86467,87623,-1,0.0878653961575928,7.42843749315945

This is a comma-delimited file that contains the following columns

• Chromosome (string)
• Start position (integer)
• Stop position (integer)
• Chromosome Strand (1 or -1)
• Measurement Value must be between [1-0] (real number; inclusive)
• Second Value (OPTIONAL): can store a second value such as an expect value (real number)