CD Genomics Bioinformatics Services FAQ

Below is a comprehensive FAQ (Frequently Asked Questions) for CD Genomics bioinformatics services, categorized by service type to help you better understand our offerings and processes.

I. Project Initiation and Management

• 1. How do I initiate a bioinformatics project?

  • To start a project, the first step is to sign a project proposal. Once signed, we will assign a project manager and a lead analyst to your project. The project manager is responsible for organizing data transfer and managing the data generation process if needed.

• 2. How will project communication be handled?

  • We will establish clear communication channels based on the project and your requirements. The frequency of communication will be adjusted according to the project's complexity and your preferences.

• 3. How can I learn about your service process?

  • You can learn more about our service process by visiting our provided links or contacting customer service. We offer detailed project progress updates and method descriptions to ensure you are always aware of the project's status.

II. Data Generation and Management

• 4. Does CD Genomics provide data generation services?

  • We can analyze data generated by your laboratory or third-party sources. Additionally, we offer extensive public domain and database data mining and analysis services. If you have not yet generated data, we can provide experimental design suggestions and assist in selecting the most appropriate technologies.

• 5. What data formats can I submit?

  • We accept most data formats, including FASTq, BAM, Excel, and others. Data can be submitted via email, cloud transfer, or physical transfer via hard drive, depending on the file size.

III. Data Analysis

• 6. What bioinformatics services does CD Genomics offer?

  • We provide a comprehensive range of bioinformatics analysis services covering multiple omics fields such as genomics, transcriptomics, proteomics, and metabolomics. Specific services include:

    • High-throughput sequencing data analysis (RNA-seq, ChIP-seq, ATAC-seq, etc.)
    • Single-cell sequencing data analysis
    • Metagenomics analysis
    • Genome variation analysis (SNV, INDEL, CNV)
    • Differential expression analysis
    • Proteomics data analysis
    • Metabolomics data analysis
    • Pathway analysis
    • Biological network construction and analysis
    • Custom workflow development

    We also handle non-omics data, such as clinical information.

• 7. What specific biological problems are you specialized in analyzing?

  • We specialize in solving the following biological problems:

    • Disease mechanism research
    • New drug target discovery
    • Microbiome research
    • Tumor heterogeneity analysis
    • Cell development processes
    • Personalized medicine
    • Environmental microbiome monitoring
• 8. What types of raw data do you accept?

  • We accept various types of raw data generated from high-throughput sequencing platforms, including Illumina, PacBio, Nanopore, etc. We also support other types of omics data such as mass spectrometry data, metabolomics data, and more.

• 9. How large-scale data can you handle?

  • We have robust computational resources that can handle massive high-throughput sequencing data, ensuring efficient and accurate analysis.

• 10. What types of analysis reports do you provide?

  • Our analysis reports typically include:

    • Quality control reports
    • Data visualization results
    • Statistical analysis results
    • Biological conclusions
    • Customized reports
• 11. How do I start a bioinformatics analysis project?

  • You can contact us via email or online form, providing detailed information about your experimental design, sample details, and data type. We will tailor a personalized analysis plan based on your needs.

• 12. What is the typical project turnaround time?

  • The project duration depends on the data complexity and analysis content. Generally, small projects can be completed within a few weeks, while larger projects may take several months.

• 13. What tools and software do you use for data analysis?

  • Our analysis primarily uses R and Bioconductor, with results exported via markdown and other tools. We provide comprehensive methods and results reports to ensure transparency and reproducibility of the analysis.

• 14. What study designs can you handle?

  • We handle various study designs, including preclinical cell or animal experiments, and clinical trials with human samples. We design suitable analysis methods based on your study type, such as multiple group comparisons or time-point analyses.

• 15. What is the typical data analysis process?

  • The analysis process varies per study, but generally includes the following steps:

    • Study Design: Confirm experiment type, number of treatment groups, dose groups/time points/cycles, etc.
    • Data Type and Format: Confirm data type (RNAseq, proteomics, etc.), platform, instrument, and data format (e.g., FASTq, BAM).
    • Analysis Content: Select appropriate analysis methods based on data and study needs, such as differential expression analysis, pathway enrichment analysis, etc.

IV. Reporting and Results Presentation

• 16. How do I receive the report after analysis completion?

  • We will send the data analysis report upon project completion and provide it as a secure, interactive HTML link. The report includes all methods and results used. Additionally, we can provide interim updates, such as quality control (QC) reports, if agreed upon beforehand.

• 17. What are the features of your reports?

  • Our reports are easy to navigate and interactive, allowing clients to explore data according to their needs. Our analysis emphasizes not just data tables but also interpreting the analysis to help you extract maximum value from your data.

• 18. Can I view sample reports?

  • Yes, we offer various sample analysis reports covering gene expression, methylation, proteomics, and more. You can contact us via email to request sample reports; please specify your area of interest, and we will try to provide relevant examples.

V. Custom Services

• 19. Do you offer customized data analysis services?

  • Yes, we offer highly customized data analysis services. We recognize that each client's needs are different, and our analysis services are tailored to the specific research goals of the client. Our team will work closely with you to ensure that the analysis results meet your research needs and expectations.

• 20. Can analysis requirements be modified during the project?

  • We understand the dynamic nature of research, so if new data or analysis needs arise during the project, we can adjust the analysis plan. At project initiation, we will clearly communicate with you to ensure that all analysis steps can flexibly accommodate potential changes.

• 21. Can you assist with multi-omics data integration analysis?

  • Yes, we excel at handling complex multi-omics datasets, including genomics, transcriptomics, proteomics, metabolomics, and more. Our team has extensive cross-omics analysis experience and can help you integrate different levels of data to provide comprehensive biological insights.

VI. Project Quality and Security

• 22. How does CD Genomics ensure project quality?

  • We have a formal Quality Management System (QMS) that has been audited by clients. The QMS ensures that we adhere to best practices internally and continuously improve while delivering excellent service to our clients. The requirements of our QMS are also available for external sharing to help clients understand our commitment to quality control and customer satisfaction.

• 23. What does your Quality Management System (QMS) include?

  • Our QMS covers standard operating procedures, data management standards, customer communication records, and project review mechanisms for all projects. The QMS aims to ensure that all projects meet the highest quality standards, and we conduct regular internal audits and improvements to maintain consistently high-level service.

• 24. How do you ensure the accuracy of data analysis results?

  • We handle each client's analysis project using a collaborative team approach, leveraging the broad expertise of our technical team to ensure that we deliver the highest quality results. All analysis methods and results undergo rigorous review and validation.

• 25. How do you ensure project confidentiality and data security?

  • We take data confidentiality and security very seriously. All data is processed and stored on secure internal servers, with industry-standard firewalls and encryption. Physical data is stored in secure facilities with restricted access and records, ensuring that only authorized personnel can access it. Additionally, all data is backed up daily at both local and remote data centers, ensuring data security and recoverability.

• 26. Do you accept third-party quality audits?

  • Yes, we welcome and have accepted multiple third-party quality audits from clients. Our QMS is open, and we are willing to demonstrate the strict standards we maintain in quality control and service delivery to build client trust.

VII. Other Common Questions

• 27. What post-analysis services do you offer?

  • We offer comprehensive post-analysis services, including:

    • Interpretation of analysis results
    • Technical support
    • Guidance on manuscript writing
• 28. What are your pricing standards?

  • Our pricing is determined based on the project's complexity, data volume, and analysis content. You can contact us to receive a detailed quote.

• 29. Do you have publications or case studies available for reference?

  • Yes, we have collaborated with several clients to publish multiple papers and conference posters covering gene expression analysis, microbiomics, and other fields. You can refer to our publications page at CD Genomics Publications.

• 30. Can you assist with experimental design and technology selection?

  • We not only provide data analysis services but also assist with experimental design and technology selection. Our team can offer recommendations based on your research goals, choosing the most suitable experimental methods and technology platforms to ensure high-quality data and successful experiments.

• 31. Do you provide interim reports or progress updates?

  • Yes, depending on the project requirements and your needs, we can provide interim reports or progress updates during the project, such as quality control (QC) reports. These updates help you stay informed about the progress of data