Data Store

Data Store represents four different data types, i.e. Sequence Data, References, Annotations, and Metadata.

• Sequence Data
• References
• Annotations
• Metadata

Sequence Data

Sequence Data stores the sequencing data files uploaded by the users and displays them in reverse chronological order. Click the icon in the Utilities menu to access the Sequence Data window (Fig. 1). The paginated window displays 10 samples, by default, per page and can be increased to show 20, 40, 60, 80, 100 samples. The search box (Fig. 1) on the top right corner allows users to filter samples with tags, organism names, or pairing information. Validation failed samples are greyed out and displayed with a “Validation Failed” message. The failed samples are not available for selection and should be deleted from the platform by the user. Validation passed samples are shown with a green check . The quality (fastqc) report is available for the validated samples (Fig. 1).

The list view shows eight fields :

• Name: Derived sample name from the file name by the platform

Example:

• Organism: Organism name, provided by the user during upload
• Tag: Tag name, provided by the user during upload
• Fastqc Reports: The FastQC quality report of each sample
• File(s): The actual file name(s) associated with the sample name
• Paired: Sample pairing information, provided by the user during upload
• Owner: Name of the user, who uploaded the samples
• Date: Date of upload

Additional sample details can be accessed by clicking on the sample name. Click the icon on the top right corner of the sample window (Fig. 2) to delete the selected sample. Click theicon to go back to the Sequence Data window.

 

References

Click the References tab after clicking the icon to access the References window (Fig. 1). The References window shows the list of validated genomes and transcriptomes for several model organisms. Validated references are also pre-indexed for commonly used tools such as Bowtie2, and Samtools and are shown as “Stanome” owned (Fig. 1). The account username is the owner of the custom references. The paginated window displays 10 references, by default, per page and can be increased to show 20, 40, 60, 80, 100 references. The search box (Fig. 1) on the top right corner of the page allows users to filter references using organism name, reference version, owner, or reference file name. Custom references are validated for file integrity, format, and content. Validation failed references are greyed out and displayed with a “Validation Failed” message. The failed references are not available for selection and should be deleted from the platform by the user.

The list view shows six columns:

• Organism: The organism name
• Owner: Validated and indexed references are owned by stanome whereas the custom references are owned by users
• Version: The version number of the reference file(s). Users can choose the version name for the custom references
• Date: Date of upload
• Genome: Name of the genome file
• Transcriptome: Name of the transcriptome file

Additional reference details (Fig. 2) can be accessed by clicking on the organism name. Click the icon on the top right corner to delete a reference. Click the icon to go back to the References window.

 

Annotations

Click the Annotations tab after clicking the icon to access the Annotations window (Fig.).  The Annotations window shows the list of the annotation files, which are utilized in the functional annotations applications, such as 

• • • Gene Models (GFF/GTF);
    • Pathway (GMT); 
    • Gene Ontology (GO);
    • Antibiotic Resistance (ABR); and 
    • Variant Effect Predictor (VEP).
    • Variations

The paginated window displays 10 annotations, by default, per page and can be increased to show 20, 40, 60, 80, 100 annotations. The search box (Fig.) on the top right corner of the page allows users to filter annotations with file names, type, organism name, or version. During upload, the annotation files undergo a rigorous validation process for file format, integrity, and content.

Examples: 

• • • Gene Models should be compatible with the reference genome version.
    • Pathway and Gene Ontology files are validated against the corresponding Gene Models. 

Validation failed annotations are greyed out and displayed with a “Validation Failed” message. The failed annotations are not available for selection and should be deleted from the platform by the user.

 

 

 

The list view shows seven fields :

• Name: Filename
• Organism: Organism to which annotation file corresponds to
• Version: Reference version to which the annotation file is associated
• Validation: Version of the annotation file
• FileType: Type of the file (Example: Pathway, GO, or VEP)
• Owner: Owner of the file
• Date: Displays the file upload date

 

 

Metadata

Click the Metadata tab after clicking the icon to access the Metadata window (Fig.).  The Metadata window shows the list view of Gene lists, Hotspots and Amplicon ranges uploaded by stanome or the user. These files are used as metadata during analysis. The window is restricted to display 10 (or more) Metadata files per page. The search box (Fig.) on the top right corner of the page allows users to filter files with name(s), type (i.e. gene list or hotspots), platform, or organism name. Metadata files are also checked for format and file integrity and their correspondence to a reference genome version. Only the validated files are available for consumption on the platform, and the remaining will be greyed out with the “Validation Failed” message.

The list view shows following six fields :

• Name: Filename
• Organism: Name of the organism to which metadata belongs to
• Reference Version: Reference version to which metadata file correspond to
• FileType: Type of the file e.g. Gene list, Hotspots, or Amplicon range
• Owner: Owner of the metadata file
• Date: Date of upload