Frequently Asked Questions

Common questions about Trovomics

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General

  • Trovomics is an online platform that analyzes omics data to provide highly interactive and customizable visualizations for research professionals looking to extract the most pertinent results from their sequencing data for the greatest impact on biological studies.

    Trovomics will take you from raw data to visualization in 3 easy steps:

    1. Create an experiment

    2. Create an analysis

    3. Visualize your results!

  • Trovomics currently has pipelines to analyze and visualize transcriptomics, or RNA-Sequencing (RNA-Seq) data. However, we are working to add additional pipelines for other omics data in the future!

  • RNA Sequencing, or RNA-Seq, uses next generation sequencing technology to (1) identify RNA by its base pair sequence and (2) quantify RNA expression in a biological sample at the time of collection. It is a technique used to gain an understanding of the transcriptome and how it may affect phenotype.

  • Yes, Trovomics offers 1-on-1 consultations with one of our computational biologists. Speak with one of our experts to learn the best way to set up your cell culture, animal, or human subjects experiment for RNA-Seq, determine how many samples to have, identify the best analysis workflows for your data, discuss how the visualizations explain your data, and much more. To schedule a consultation, please contact us through our Support Request Form.

  • In the methods section describing your sequencing analysis and visualization, please include:

    “Raw sequencing data was analyzed and visualized using Rajant Health Incorporated’s Trovomics omics analysis service (www.trovomics.com).”

    The auto-generated methods available for download in Trovomics can be used as a guide for writing detailed methodology of any visualizations you included in your manuscript.

  • We currently only support sequencing files from Illumina sequencing platforms. However, we are working to support additional platforms in the future!

  • Yes! Access to the Trovomics Demo Environment is free and comes preloaded with sample data sets that you can use to explore the platform’s basic controls and visualizer functionality. You can create your account for free and familiarize yourself with the platform at your own pace. No time limitations or expiration dates to worry about. When you’re ready to work with your own data inside of Trovomics, simply upgrade your account access.

Processing and Analysis

  • At a minimum, RNA-Seq data analysis requires the following steps, performed through various scripts and code, in order to understand the results of your experiment:

    • Map your short (or long) sequence reads against a reference genome of your desired species.

    • Quantify the expression of genes.

    • Compare the expression of genes across your biological samples or different variables.

    • Interpret the functional impact of any differentially expressed genes.

    • Generate graphs to visualize the analyses

    Alternatively, you could use Trovomics to analyze and visualize your RNA-Seq data to significantly streamline the process. No prior coding experience necessary.

  • Trovomics has built a robust pipeline that uses various industry-standard tools to perform quality control, gene quantification, differential expression analysis, and functional analysis on your RNA-Seq samples. Below is a list of packages that we use to analyze your data:

    • Quality control: FASTQC, AdapterRemoval

    • Mapping/Alignment: HISAT2

    • Gene quantification: HTseq

    • Differential expression: DESeq2

    • Functional analysis: clusterProfiler

      • Knowledge databases: Gene Ontology

    In addition, our computational biologists have implemented proprietary scripts to enhance and automate the pipeline.

  • Analysis of your RNA-Seq data may take up to 48 hours* in Trovomics, depending on how many samples you have in your experiment, what type of analysis you’re running, and available resources. Once completed, all seven visualization types are available for viewing and customization.

    *Processing time may be affected by the volume, complexity, and quality of the data submitted for analysis.

  • The difference between Trovomics and R is that in Trovomics you don’t need to write code to analyze and visualize your RNA-Seq data like you do in R. You can rely on Trovomics’s standardized pipeline of industry-proven tools, selected by our computational biologists, to analyze your data at the click of a button. If you were to take the time to code your analysis in R using the same parameters you selected in Trovomics, you would get the same results. Trovomics saves you time and requires no coding experience.

File Uploads / Downloads

  • We accept your sample files in .FASTQ format. However, the file names must be in Illumina’s original naming convention, as received from Illumina. Files downloaded from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) must have filenames as they are downloaded from Sequence Read Archive (SRA). If file names are altered, then vital sample information could be lost.

    Read more about Illumina’s Naming Conventions.

    For single-ended data:

    Example of Illumina’s naming convention:

    SampleName_S1_L001_R1_001.fastq.gz

    Example of NCBI GEO file names:

    SRR12345678.fastq.gz

    For paired-ended data:

    Example of Illumina’s naming convention:

    SampleName_S1_L001_R1_001.fastq.gz

    SampleName_S1_L001_R2_001.fastq.gz

    Example of NCBI GEO file names:

    SRR12345678_1.fastq.gz

    SRR12345678_2.fastq.gz

    If you believe the file names to your samples have been altered, reach out to us and we can work out a solution.

  • Gene lists and sample lists are available in a .csv format, compatible with applications like Apple Numbers® and Microsoft Excel®.

    Method files are available in a .txt format, compatible with most operating systems word processing programs.

    Images are available in .svg, .jpeg, and .png formats, compatible with all image viewing applications.

The Visualizer

  • Currently, Trovomics offers six visualizations including: Volcano plot, GO bar graph, Heatmap, Distribution plot, Scatter plot, and Comparison. The following visualization will be available in early 2024: PCA plot.

  • In Trovomics, you can filter your sample list or gene list to remove samples or genes, respectively. This can be saved as a new sample or gene list that then can be used to immediately re-generate all seven visualizations. This process is referred to as “re-analysis.” It’s easy in Trovomics and the opportunities for visualizations of your data are endless.

The Subscription Service

  • We currently accept the following forms of payment: Visa, Mastercard, Discover, and American Express. All subscription plans require a 12 month commitment and are billed on a monthly auto-renewing schedule. Billing statements are sent to the account holder’s email each month. Monthly statements are also available for download.

  • If you have access to our Demo Environment, you can upgrade your access from the Main Dashboard. Go to your Account Profile and select “Plan & Billing.” From there you will be able to upgrade to a subscription-based account.

    If you have a Basic subscription plan, you can upgrade your access to Pro or Enterprise level by logging into your account and submitting a Support Request form. You can also contact our sales team Monday - Friday from 9:00 AM - 5:00 PM EST at +1 (484) 595-0233, extension 350.

  • At this time, you cannot invite collaborators or share data within the Trovomics platform. Files must be downloaded and shared independently of the platform for any collaborations.

Information and Data Storage

  • Only you have access to your raw data and results.

  • If your subscription plan ends and is not renewed within 30 days, your data will be deleted.

Customer Support

  • Our Help Center is always at your fingertips with a variety of Trovomics documentation and other bioinformatics resources to assist you 24/7.

    Subscription holders also have access to 1-on-1 Trovomics consultations to support you in all steps of your omics journey while using the platform.

    If you need to contact our customer support team, log in to your account to submit a help request through our Support Form and a team member will respond within 2 business days. If you need to speak directly with someone, you can call us Monday – Friday, from 9:00 AM – 5:00 PM EST at: +1 (484) 595-0233, extension 350.

Don’t see what you’re looking for here?

Check out additional resources in our Help Center.

Need to talk to an expert?

Some things require a little more troubleshooting. We’re happy to help. Log in to your account to submit a support request and a member of our team will be in touch.