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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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| == Inputs ==
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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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| === 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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| *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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| ==== 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:
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| 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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