Difference between revisions of "LoadExperiment"

Revision as of 15:20, 3 March 2014

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

Inputs

Metadata

• 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

• Note: Additional metadata about the experiment can be added as well.
  • Example from an experiment loaded into EPIC-CoGe: http://genomevolution.org/CoGe/ExperimentView.pl?eid=193
  • Information on providing a metadata file for bulk import: Experiment Metadata

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

Each of these file formats are described below in their own section. The file type can be auto-detected by LoadExperiment if the file name ends with the expected extension (.csv, .tsv, .bed, .vcf, .bam). Files can be compressed (.zip, .gz) and still have their type auto-detected (e.g., mydata.bed.gz). For non-standard file name extensions, you can select the file type from a list.

CSV File Format

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)

#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

TSV File Format

Same as CSV format but with tab delimiters instead of commas.

BED File Format

Standard BED format as defined here: http://genome.ucsc.edu/FAQ/FAQformat.html#format1

Only the first six columns are used, with the "name" field ignored.

GFF File Format

Standard GFF3 format as defined here: http://gmod.org/wiki/GFF3

Only the seqid, start, end, score, and strand columns are used (column numbers 1, 4, 5, 6, 7 respectively).

VCF File Format

Standard VCF 4.1 format as defined here: http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41

BAM File Format

Standard BAM format.

Bulk Loading

Please contact the CoGe Team if you have many experiments you wish to load. We will help you with the bulk loading.