RNA sequencing pipeline

In silico analysis of transcriptomes to accelerate the discovery and development of therapeutic solutions

RNA sequencing has transformed the research approach to investigating gene expression. It employs high-throughput sequencing techniques to provide deeper insights into a cell’s transcriptome. At Aganitha, we incorporate the latest technologies to make RNA sequencing pipelines scalable and efficient while ensuring accurate transcriptomic profiling. In addition, our multidisciplinary teams provide seamless integration of our services and solutions into the drug discovery and development process.

Our RNA sequencing service catalog offers the following:

End-to-end RNA services for both Bulk RNA sequencing analysis and Single Cell RNA sequencing analysis

On-demand customizable Biomarker detection services


Key components of our RNA sequencing service:

End-to-end analysis

Our pipeline allows end-to-end data analysis with minimal user intervention while assisting and guiding beginner in RNA seq analysis

Cell type annotation

Expression profiles in the data are evaluated using existing and ensemble models for more accurate identification of cell type and subtype clusters

Marker analysis

Identify markers in a ranked order for further evaluation in the exploratory analysis pipeline. Scientists have a greater degree of control in defining and changing parameters

MoA evaluation

Identify the mechanism of action(MoA) in both the disease and treatment options. Data pertinent prediction for responder versus non responders to treatment in patient populations

Customizable pipeline

We provide multiple options for each part of the analysis pipeline giving the flexibility to the scientists to customize the pipeline according to their needs
The RNA sequencing pipeline starts with the pre-processing step which is processing raw data to provide the resulting count matrices after removing any low-quality leads through the quality control, data correction, normalization, and feature selection steps. The next steps are clustering and cluster annotation. The resulting count matrices can then be used for downstream analyses like differential expression, compositional analysis, and trajectory inference. The results from downstream analysis can further be used to produce gene dynamics, fold enrichment, and enrichment analysis reports.
RNA Sequencing Pipeline

Differentiators and Values

Our technological skills and domain-specific expertise in RNA Sequencing serve as our differentiators helping us build quality solutions with a quick turnaround time, delivering a superior customer experience

Functional Differentiators

Default end-to-end analysis pathways

  • Default analysis pathways help bioinformaticians derive their analysis faster
  • Configurable user-defined analytical pathways for advanced bioinformaticians

Custom pluggable modules

  • Relevant alternatives for each section of the RNA seq analysis pipeline are evaluated and made available on demand
  • Multiple analysis options available with customizable modules for cell annotation and identification, cell type clustering, enrichment analysis, differential expression, and co-expression, among others

Statistical analysis visualizations

  • Rich visualizations ranging from simple scatter plots to complex UMAPs are available on demand
  • Interactive visual plots elucidate analysis and track changes to downstream plots

Enhanced data security and capability

  • Highest norms of data protection systems and procedures to keep data secure
  • Cloud-based IT infrastructure for expanding existing RNA seq capabilities

Smart resource consumption

  • Optimized allocation of computationally intensive tasks to minimize resource utilization
  • Data caching to prevent unforeseen run failures saving time

Enhanced experience and productivity

  • User-friendly and interactive
  • Processing multiple RNA sequences in parallel
  • Ability to process multiple user requests on a single deployed RNA sequence pipeline

Technology Differentiators

Discover our offerings across the biopharma value chain

Learn more about our RNA sequencing pipeline