LoadExperiment: Difference between revisions

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


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


===Data File===
=== Data File ===
You can select and retrieve data file located at:
 
*The iPlant Data Store
You can select and retrieve data file located at:  
*An FTP server
 
*Your computer (Upload)
*The iPlant Data Store  
*An FTP server  
*Your computer (Upload)<br>


===Data File Name Extension===
=== Data Formats ===
'''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'
LoadExperiment supports several data file formats depending on the data type:
 
*Quantitative data
**Comma-separated (CSV) file format
**Tab-separated (TSV) file format
**BED file format
*Polymorphism (SNP) data
** Variant Call Format (VCF) file format
*Alignment data
** BAM file format
 
==== CSV File Format ====
The data format is very important! Here is an example set of data:  


===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)
  #CHR,START,STOP,STRAND,VALUE1(0-1),VALUE2(ANY-ANY)
  Chr1,11486,12316,1,0.181430277220112,7.3980806218146
  Chr1,11486,12316,1,0.181430277220112,7.3980806218146
Line 33: Line 46:
  Chr1,86467,87623,-1,0.0878653961575928,7.42843749315945
  Chr1,86467,87623,-1,0.0878653961575928,7.42843749315945


This is a comma-delimited file that contains the following columns
This is a comma-delimited file that contains the following columns  
*Chromosome (string)
 
*Start position (integer)
*Chromosome (string)  
*Stop position (integer)
*Start position (integer)  
*Chromosome Strand (1 or -1)
*Stop position (integer)  
*Measurement Value must be between [1-0] (real number; inclusive)
*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)
*Second Value (OPTIONAL): can store a second value such as an expect value (real number)

Revision as of 18:51, 30 October 2013

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

Inputs

  • 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 Formats

LoadExperiment supports several data file formats depending on the data type:

  • Quantitative data
    • Comma-separated (CSV) file format
    • Tab-separated (TSV) file format
    • BED file format
  • Polymorphism (SNP) data
    • Variant Call Format (VCF) file format
  • Alignment data
    • BAM file format

CSV File 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)
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