SNPDB»IMPORT
Log in to 'GENica Marker Tools'
Description
- Use the SNPDB»IMPORT option to upload single nucleotide polymorphism data for your research projects into SNPDB.
- During import, markers that do not already exist in the snpmarker-type marker set called "SNP Markers (MPBCRC:public:mhayden)" in the MARKERS Table are linked to a generic "unknown" marker in "SNP Markers (MPBCRC:public:mhayden)".
- Once imported, use SNPDB»SEARCH or SNPDB»BROWSE to search and, if required, edit the stored data.
Back to contents
How to use this option
- Click on BROWSE to locate the input file to be uploaded.
- Identify a project in which the data is to be stored from the "Project/Group" pull-down menu. The menu displays the names of projects a user has access to, followed by the projects' user group names in brackets. Click on the [ADD PROJECT] link to create a (new) project. (Please also refer to the section on SNPDB»BROWSE.)
- Select the genotyping platform from the "Platform used" pull-down menu.
- Select a Species from the dropdown list. Click on the [ADD SPECIES] link to create a (new) SPECIES.
- The Species dropdown list contains the species information stored in GMT, being: the common name, the NCBI taxonomy ID and the full name. GMT-stored species information can be viewed at ADMIN»SPECIES and NCBI searches can be performed by clicking the [NCBI] button on that page.
- Click on IMPORT to begin uploading the file. This may take some time, depending on the size of the input file.
- An import report appears, giving details on the run that has been created.
Click on the [DELETE UPLOAD] link if the wrong file has been imported.
Click on the [DOWNLOAD IMPORT LOG] link if you wish to save an import log for future reference.
- After reviewing the import report, click on the FINISHED button to complete the SNPDB»IMPORT. This will bring up the SNPDB»BROWSE interface, please refer to the SNPDB»BROWSE manual section for details.
Back to contents
The SNPDB»IMPORT input file
- The input file should be structured like the following.
Input Sample
| Well | Type | Sample | ASPEname | SNPname | AR values | Genotypes | Plate ID | Acquisition Date | Platform
|
| C1 | X3 | MUNDAH | HvSNP.159a | Bmy1_R115C_115[G/A]bot | 0.91 | gg | Matt | 19-Mar-2007 | LX10005220302
|
| D1 | X4 | TILGA | HvSNP.159a | Bmy1_R115C_115[G/A]bot | 0.00 | aa | Matt | 19-Mar-2007 | LX10005220302
|
| E1 | X5 | VB9926 | HvSNP.159a | Bmy1_R115C_115[G/A]bot | 0.00 | aa | Matt | 19-Mar-2007 | LX10005220302
|
An example file so you can try uploading data (SNPDB_import_example.txt) can be found here (GENica Marker Tools login required).
The fields required are:
| Field Heading | Description | Field requirements
|
| Well | Well address on the 96-well plate | Optional data, leave empty if not present
|
| Type | Use the following abbreviations to identify sample "types":
"X" for "Sample"; if more than one sample, distinguish by adding consecutive numbers, e.g. X1, X2, X3, etc.
"B" for "Background"; if more than one well is used for background correction, distinguish by adding consecutive numbers, e.g. B1, B2, B3, etc.
"+C" for "Positive Control"; if more than one positive control, distinguish by adding consecutive numbers, e.g. +C1, +C2, etc.
"-C" for "Negative Control"; if more than one negative control, distinguish by adding consecutive numbers, e.g. -C1, -C2, etc.
"S" for "Standard"; if more than one standard, distinguish by adding consecutive numbers, e.g. S1, S2, etc. | Optional data, leave empty if not present
|
| Sample | Name of the sample being assayed in a well | Required data, an entry must be made. If samples are being genotyped on multiple plates (eg different groups of binned SNPs), the sample name for each sample must be the same in all files imported into a project. No two genetically distinct samples should share the same Sample name within a project.
|
| ASPEname | Internally used SNP name | Required data, an entry must be made. If a marker is listed in marker set SNP Markers (MPBCRC:public;mhayden), using its exact "ASPEname" enables the database to link marker and genotype information.
|
| SNPname | Published SNP name | Required data, an entry must be made. If a marker is listed in marker set SNP Markers (MPBCRC:public;mhayden), using its exact "SNPname" enables the database to link marker and genotype information.
|
| AR value | "Allele Ratio" value used to determine the genotype in OLA or ASPE assays | Optional data, leave empty if not present.
|
| Genotypes | Sample genotype, e.g. "gg", "ga", "aa", etc. | Optional data, leave empty if not present
|
| Plate ID | A unique identifier for the plate / run | Required entry. The PlateID can be either provided in the import file, OR through a text box on the SNPDB»IMPORT page.
|
| Acquisition Date | Date the assay was performed, please follow format dd-<three first letters of month>-yy, e.g. "19-Mar-07" | Optional data, leave empty if not present
|
| Platform | Genotyping machine used | Optional entry. The platform entry can be either provided in the import file OR through a drop-down box on the SNPDB»IMPORT page.
|
When creating a SNPDB import file, the following conditions are in force:
- All field headings are required.
- Sample, ASPEname, SNPname should have values.
- Data should be present for Plate Identifier (if not it should be entered into the SNPDB»IMPORT input form).
- Platform can be in the file, or entered in the input form. If not in the file, the value from the form will be used.
- All other fields can have null values. "Missing" genotypes (ie, Sample by ASPEname/SNPname combinations where there was an assay performed but no sound genotype discovered) should be expressed as an empty cell.
Back to contents
Links to other user manual pages
I'd rather try the tutorial...
|
