LoadExperiment

LoadExperiment enables you to load a file 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

Enter metadata that describes the experiment

• 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 to associate file with
• 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 Files

Select data files

You can select and retrieve data file located at:

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

Note: Typically only a single data file can be selected. The exception is FASTQ formatted files for which multiple files can be selected.

Data Formats and Track Types

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

• Quantitative data
  

  Quantitative track
  • Comma-separated (CSV) file format
  • Tab-separated (TSV) file format
  • BED file format
  • WIG file format
• Marker data
  

  Marker track
  • GFF/GTF file format
• Polymorphism (SNP) data
  

  SNP track
  • Variant Call Format (VCF) file format
• Alignment data
  

  Alignment track
  • BAM file format
  • FASTQ 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 [0-1] (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

Two types are supported:

• 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.
• BedGraph format as defined here: http://genome.ucsc.edu/goldenPath/help/bedgraph.html

Note that the 0-based coordinates of the BED format will be translated into 1-based within CoGe. Measurement values must be between [0,1].

WIG File Format

Standard WIG format as defined here: http://genome.ucsc.edu/goldenpath/help/wiggle.html

Only the "variableStep" type is supported. The "fixedStep" type is not supported and will cause the load to fail with an error.

Start and end coordinates are expected to be 1-based. Measurement values must be between [0,1].

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.

FASTQ Data

EPIC-CoGe now supports fastq data generated by RNASeq. When loaded, EPIC-CoGe will run and the Expression Analysis Pipeline developed by James Schnable for his qTeller project.

Troubleshooting

Make sure that these basic requirements are followed:

• The file format must be one of those listed above.
• The chromosome names used in the data files exactly match those for the genome. Mismatches will cause the load to fail.
• For text files, such as .CSV and .VCF, the newline (EOL) characters must be Unix-compliant (LF character, not CRLF) , see this article. This is sometimes a problem when loading text files created in Excel on Windows OS.

Bulk Loading

Please contact the CoGe Team if you have large numbers of experiments you wish to load and we can help you with the bulk loading.