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| − | 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]].
| + | #REDIRECT: [[LoadExp+]] |
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| − | [[File:LoadExperiment.png|thumb|400px]]
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| − | == Inputs ==
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| − | === Metadata ===
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| − | *'''Name:''' Name of experiment
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| − | *'''Description:''' Description of experiment
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| − | *'''Version:''' Version of experiment
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| − | *'''Source:''' Where is the data from? This could be you, your lab, your university, a sequencing center, your collaborator.
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| − | *'''Restricted:''' Is this experiment public or restricted to you and your collaborators
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| − | *'''Genome:''' Select the appropriate genome from CoGe
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| − | *'''Select Data File:''' Opens a window for specifying the input data file
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| − | *'''Note''': Additional metadata about the experiment can be added as well.
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| − | ** Example from an experiment loaded into EPIC-CoGe: http://genomevolution.org/CoGe/ExperimentView.pl?eid=193
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| − | ** Information on providing a metadata file for bulk import: [[Experiment Metadata]]
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| − | === Data File ===
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| − | You can select and retrieve data file located at:
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| − | *The iPlant Data Store
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| − | *An FTP server
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| − | *Your computer (Upload)<br>
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| − | === Data Formats ===
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| − | LoadExperiment supports several data file formats depending on the data type:
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| − | *Quantitative data
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| − | **Comma-separated (CSV) file format
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| − | **Tab-separated (TSV) file format
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| − | **BED file format
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| − | *Marker data
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| − | ** GFF/GTF file format
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| − | *Polymorphism (SNP) data
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| − | **Variant Call Format (VCF) file format
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| − | *Alignment data
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| − | **BAM file format
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| − | 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.
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| − | ==== CSV File Format ====
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| − | This is a comma-delimited file that contains the following columns
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| − | *Chromosome (string)
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| − | *Start position (integer)
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| − | *Stop position (integer)
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| − | *Chromosome Strand (1 or -1)
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| − | *Measurement Value must be between [1-0] (real number; inclusive)
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| − | *Second Value (OPTIONAL): can store a second value such as an expect value (real number)
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| − | #CHR,START,STOP,STRAND,VALUE1(0-1),VALUE2(ANY-ANY)
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| − | Chr1,11486,12316,1,0.181430277220112,7.3980806218146
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| − | Chr1,27309,28272,1,0.944373742485446,5.08225285439412
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| − | Chr1,32484,32978,1,0.328500324191726,1.97719838086201
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| − | Chr1,41942,42508,-1,0.825027233105203,6.56057592312617
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| − | Chr1,56394,57527,-1,0.183234367788511,0.795527328556531
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| − | Chr1,67705,68809,-1,0.956523086778851,5.20992343466606
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| − | Chr1,71144,72409,1,0.42955128220331,1.80604269639474
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| − | Chr1,81671,82833,1,0.626003507696723,2.77834108023821
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| − | Chr1,86467,87623,-1,0.0878653961575928,7.42843749315945
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| − | ==== TSV File Format ====
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| − | Same as CSV format but with tab delimiters instead of commas.
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| − | ==== BED File Format ====
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| − | Standard BED format as defined here: http://genome.ucsc.edu/FAQ/FAQformat.html#format1
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| − | Only the first six columns are used, with the "name" field ignored.
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| − | ==== GFF File Format ====
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| − | Standard GFF3 format as defined here: http://gmod.org/wiki/GFF3
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| − | Only the seqid, start, end, score, strand, and attribute columns are used (column numbers 1, 4, 5, 6, 7, 9 respectively).
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| − | ==== VCF File Format ====
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| − | Standard VCF 4.1 format as defined here: http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41
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| − | ==== BAM File Format ====
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| − | Standard BAM format.
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| − | ==Bulk Loading==
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| − | Please contact the [mailto:coge.genome@gmail.com CoGe Team] if you have many experiments you wish to load. We will help you with the bulk loading.
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