RegionMiner subtask: Upload data into ElDorado

Introduction

This task takes genomic regions as input and uploads the data into the ElDorado database at Genomatix. The data will appear in the "user-specific data" section on the start page of ElDorado and can be selected for viewing in the detailed graphics page. This way the region can be visualized and evaluated within the context of the surrounding genome.
A maximum of 10 user-defined data sets with up to 100,000 regions each can be uploaded. The data sets can be deleted via the personal page of the user.

Note, that the data can only be seen within the account that was used for the upload.

Parameters

Input
Input	Input data are accepted as a tab delimited file in BED file format containing the input regions specified at least by chromosome number, start position and end position (in this order). The maximum amount of regions and their maximum length can differ for various tasks. The limits are usually shown on top of the input pages. Within this section you can either choose from previously uploaded BED files upload a new one If you're uploading a new file, you'll have to choose the correct organism for the BED file, as the organism is associated with the BED file for future use (the default is the latest setting in the current session). Note that almost all browsers have a general upload limit of 2 GB, i.e. BED files bigger than this size should be zipped before uploading. Optionally you can specify the name that is used to save the file on the server, otherwise the name of the uploaded file will be used. If any of the regions in the input file can not be completely assigned to the selected genome (e.g. wrong chromosome numbering or wrong positions within a chromosome), an error message will appear and the regions will be skipped. Note that BED files critically depend on the underlying genome build, which can be changed by selecting a different ElDorado version on your personal page (see list of genomes available in ElDorado). To change the analysis from the mouse genome NCBI build 37 to build 36, for example, ElDorado 05-2007 should be selected. You may also choose to NOT save a file on the server. If you use this option, the file will be used for the selected task but won't be available for subsequent analyses. Uploaded BED files can be deleted from the project anytime via the project management. If the checkbox "Ignore duplicates" is activated, all regions with the same chromosome, start and end position and same strand will be reduced to one data point, i.e. the number of uploaded data points can be smaller than the number of regions in the input file.
Identification of data
Identification	The uploaded data will be identified with a corresponding label and description. The label will be used for displaying the elements in the graphic components of ElDorado, the description is additionally used for selection of user-defined data. Note that the label must be unique within the set of your uploaded data, otherwise a warning will appear.

Input

Input data are accepted as a tab delimited file in BED file format containing the input regions specified at least by chromosome number, start position and end position (in this order).
The maximum amount of regions and their maximum length can differ for various tasks. The limits are usually shown on top of the input pages.

Within this section you can

either choose from previously uploaded BED files
upload a new one

If you're uploading a new file, you'll have to choose the correct organism for the BED file, as the organism is associated with the BED file for future use (the default is the latest setting in the current session).

Note that almost all browsers have a general upload limit of 2 GB, i.e. BED files bigger than this size should be zipped before uploading.

Optionally you can specify the name that is used to save the file on the server, otherwise the name of the uploaded file will be used.

If any of the regions in the input file can not be completely assigned to the selected genome (e.g. wrong chromosome numbering or wrong positions within a chromosome), an error message will appear and the regions will be skipped.

Note that BED files critically depend on the underlying genome build, which can be changed by selecting a different ElDorado version on your personal page (see list of genomes available in ElDorado). To change the analysis from the mouse genome NCBI build 37 to build 36, for example, ElDorado 05-2007 should be selected.

You may also choose to NOT save a file on the server. If you use this option, the file will be used for the selected task but won't be available for subsequent analyses.

Uploaded BED files can be deleted from the project anytime via the project management.

If the checkbox "Ignore duplicates" is activated, all regions with the same chromosome, start and end position and same strand will be reduced to one data point, i.e. the number of uploaded data points can be smaller than the number of regions in the input file.

Identification of data

Identification

The uploaded data will be identified with a corresponding label and description. The label will be used for displaying the elements in the graphic components of ElDorado, the description is additionally used for selection of user-defined data. Note that the label must be unique within the set of your uploaded data, otherwise a warning will appear.