Difference between revisions of "LoadExperiment"

Revision as of 11:41, 1 April 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 and Track Types

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
• Marker data
  • GFF/GTF 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, .gff, .gtf, .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, strand, and attribute columns are used (column numbers 1, 4, 5, 6, 7, 9 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.