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Annotations: Data describing the gene models, pathways, ontologies, and other relevant biological information. Annotations are always associated with a reference genome and are consumed during a command execution through the argument or input variables. Argum...

Click (Fig. 2) from any App to open the execution dialog box. Execution requirements vary for each App but generally, three objects are expected - inputs, parameters, and outputs. Select the right objects from the drop-downs and click the Submit button. Fig...

App execution results are displayed similar to the jobs list window in a project and can be accessed by clicking the  icon (Fig 3). Fig: App jobs list view.    

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 p...

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 too...

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); Pat...

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 win...

A pipeline is defined as a set of computational tools, which run either sequentially or parallelly to achieve a specific data analysis objective. Bioinformatics tools (and their respective commands) are designated as steps within a pipeline. Stanome provides a...

Data upload is the first step in the analysis. Generally, four data types are required:  Sequencing data (read files) Reference genomes Annotation files Metadata Click the icon in the Utilities menu to access the Uploader window. Each data ty...

Sequencing files can be uploaded through the SEQUENCE DATA (Fig. 1) tab. Complete all the fields in the form before selecting the files. MatePair: Select appropriate mate-pair information, if available. This is an optional parameter (Default: No). Strand: Se...

The latest versions of reference genomes and transcriptomes are available on the platform for eight model organisms. Pre-configured references can be explored through REFERENCES (Fig.). The owner column helps to identify the pre-configured references (owned by...

Pathways, gene ontology (GO) terms, ABR genes, and VEP (Variant Effect Predictor) files are classified as annotations and can be uploaded through the ANNOTATIONS (Fig.) tab. ABR and GO_OBO upload has two fields: Organism: Name of the organism Tag: The versi...

Any files associated with an experiment (excluding sequencing files, references, and annotations) can be uploaded through the METADATA (Fig.) tab. During upload, the metadata files should always be associated with an organism and tagged appropriately, as expla...

Sample Set is a group of sequence files that belong to an experiment and can be analyzed together. Sample Set window allows new sample set creation and provides a list view of the existing Sample Sets within a project (Fig. 1).       Sample Set Creation ...

Pipelines, from any project, can be added or deleted from the favorites by clicking the icon next to the pipeline name in the list view i.e. My Pipelines. Stanome owned pipelines can’t be added to the favorites. Favorite pipelines are visible in the Pipeline ...

A new project can be created in two ways.  From the Dashboard window - click the icon From the Projects window - click on the upper right corner A new project can be created from the Project setup window (Fig. 1). Fill in the seven mandatory fields with ...

My Pipelines show the list of pipelines within a project. Pipelines can be created, viewed, edited, and deleted within the project scope. My Pipelines is empty, by default, and users can create new pipelines de novo or copy the pre-configured pipelines from th...

The new pipeline creation window is accessed from two locations. Either click on the project window or click on the My Pipelines window to create a new pipeline (Fig. 1).     The new pipeline creation window displays three icons in the upper right corne...

Pipelines on the platform are tightly connected with the projects. The Data type field in the projects is tied with the Hub field in the pipelines. Based on the Data Type definition in the project setup, only relevant pipelines are shown. The following table s...

A new pipeline can be created by copying an existing pipeline from other projects or a pre-configured pipeline from Pipeline Library.  Click in the upper right corner of the pipeline creation window to see the existing pipelines via the Select pipeline dialog...