|
|
| (140 intermediate revisions by 4 users not shown) |
| Line 1: |
Line 1: |
| − | 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+]] |
| − | | + | |
| − | [[File:LoadExperiment.png|thumb|400px]]
| + | |
| − | | + | |
| − | == 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)<br>
| + | |
| − | | + | |
| − | === 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 [mailto:coge.genome@gmail.com CoGe Team] if you have many experiments you wish to load. We will help you with the bulk loading.
| + | |
