LoadExperiment supports several data file formats depending on the data type:
*Quantitative data [[File:quant_track.png|thumb|200px|Quantitative track]]
**Comma-separated (CSV) file format
**Tab-separated (TSV) file format
**BED file format
*Marker data [[File:marker_track.png|thumb|200px|Marker track]]
** GFF/GTF file format
*Polymorphism (SNP) data [[File:snp_track.png|thumb|200px|SNP track]]
**Variant Call Format (VCF) file format
*Alignment data [[File:alignment_track.png|thumb|200px|Alignment track]]
**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)
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.
====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 [http://qteller.com qTeller] project.
==Bulk Loading==
Please contact the [mailto:coge.genome@gmail.com CoGe Team] if you have large numbers of experiments you wish to load and we can help you with the bulk loading.
Revision as of 17:10, 16 September 2014
UNDER CONSTRUCTION
LoadBatch provides the ability to conveinently load a set of genomes or experiments in a single operation. To load a set of genomes using LoadGenome would require running the tool for each genome individually.
