Data Processing Pipelines for RNA-seq Data

RNA sequencing (RNA-seq) provides insights into gene expression levels, alternative splicing events, and the discovery of novel transcripts. This technology is essential for understanding gene function, identifying biomarkers, and exploring the complexities of cellular responses along with regulatory mechanisms. Advanced pipelines are needed to effectively process and interpret this complex data type. This blog explores the significance of efficient data processing pipelines, and the challenges involved in building them. It also highlights how Elucidata has created and offers customized solutions to facilitate efficient data processing and downstream analyses.

Advantages of Accurate and Efficient Data Processing

Accurate RNA-Seq data processing ensures reliable identification and quantification of gene expression, which is critical for downstream analyses like differential expression studies and biomarker discovery. Efficient pipelines save time and computational resources, facilitating large datasets handling and extensive studies. The streamlined processes, therefore, reduce errors and biases, along with enhancing reproducibility and robustness. The adoption of advanced RNA-Seq data processing enables greater focus on the biological insights rather than just technical issues, and accelerates scientific discovery.

Challenges in Building Data Processing Pipelines for RNA-Seq Data

A typical RNA-Seq data processing pipeline starts with quality control (QC) of raw sequencing reads, followed by read trimming to remove low-quality bases and adapters. The cleaned reads are then aligned to a reference genome or transcriptome. Finally, the aligned reads are quantified to generate count data, which represents the expression levels of genes or transcripts.

Though this might seem fairly straightforward, there are several aspects that can impact the quality and reliability of the results.

1. Choosing the Right Set of Tools

Choosing the right set of tools for RNA-seq data processing involves several critical challenges, including adapter identification and trimming, alignment, and quality control (QC). Accurate identification and removal of adapter sequences are essential to prevent biases in downstream analyses, as misidentification or incomplete trimming can lead to erroneous alignments and quantification. Aligning reads to a reference genome or transcriptome presents its own set of challenges, as it can be computationally intensive and prone to errors, particularly in repetitive or low-complexity regions. Additionally, ensuring the quality of raw and processed data through effective QC is crucial to identify and address issues such as low-quality reads, contamination, and biases. The availability of multiple tools (Trimmomatic, Cutadapt, Fastp) along with the nuances involved (adaptor removal and quality metrics) in making the right tool choice can be cumbersome and perplexing.

2. Infrastructure Related Challenges

The extensive computational power required for alignment, quantification, and quality control can require up to 128 GB of RAM and 16 CPUs, necessitating cloud-based machines or large computing clusters. Additionally, the large volume of RNA-Seq data requires robust storage solutions and efficient data transfer mechanisms, which can be both expensive and time-consuming. For example, generally processing costs range around $10 per sample, and may take a few hours or a couple of days, depending on hardware and number of samples.

These factors collectively impose a substantial burden on resources, impacting the overall efficiency and cost-effectiveness of RNA-seq data processing.

3. Quality of Counts

Quality of counts in RNA-seq is a critical challenge that affects the accuracy and reliability of gene expression quantification. Accurate quantification is essential for meaningful downstream analyses. However, technical biases, sequencing depth, and alignment errors can all compromise the quality of counts. Additionally, batch effects and technical variability, arising from differences in sample preparation, sequencing runs, and other technical factors, can further confound biological interpretations.

4. Metadata Accuracy

Accurate and consistent metadata annotation is essential to ensure the reproducibility and reliable interpretation of RNA-Seq studies. Inaccurate or incomplete metadata can lead to erroneous conclusions undermining the validity of findings. Furthermore, integrating RNA-Seq data with other omics datasets or across different studies necessitates accurate and compatible metadata to ensure data interoperability and coherence. Without consistent metadata, the integration process can be compromised, leading to potential discrepancies and difficulties in drawing meaningful comparisons or conclusions.

Elucidata’s Pipeline Solutions to Address These Challenges

Elucidata offers comprehensive pipeline solutions for data processing, designed to streamline and enhance the analysis of RNA-Seq data. Our data harmonization platform, Polly, allows users to choose from a suite of scientifically validated bioinformatics pipelines enabling processing of a variety of multi-omics data types. Alternatively, users can leverage our expertise to develop and deploy customized pipelines tailored to their specific omics data types and analysis requirements.

Elucidata’s efficiency can be assessed from its ability to perform RNA-seq data processing at scale, processing up to 5,000 samples per week with any pipeline of reasonable depth (50M reads/sample), at a significantly lower cost (three times cheaper) than the industry standard, and all without compromising on quality.

Following are the major workflow steps-

Data Preparation: RNA-Seq data is ingested into Polly from multiple sources like NCBI's Gene Expression Omnibus, and the European Nucleotide Archive. Adapters are trimmed,quality assessment and filtering is done using tools such as trimmomatic/ cut-adapt/ FastQC.
Alignment and Quantification: Polly uses advanced alignment algorithms like STAR, Kallisto, and HISAT2 (depending upon the user’s end requirement) to map RNA-Seq accurately reads to a reference genome for gene expression quantification.
Quality Control and Normalization: Polly uses FastQC, MultiQC, and edgeR for quality control and normalization. This method reduces false-positive rates by 25%, ensuring reliable results and saves researchers’ time.

What Sets Elucidata’s Solutions Apart?

Customizability: Our workflows are highly configurable to align with researchers' specific needs. Whether it's the pipeline, tools, curation fields, or ontology, our expertise allows us to customize any aspect and incorporate it into a seamless workflow. We can optimize compute capacity and workflow environments to match the users' computational requirements, and leverage workflow orchestrators like Nextflow for efficient resource management.
Speed: Our automated pipelines and scalable infrastructure enable us to process over 5,000 samples per week. Additionally, we have developed machine learning models for auto-curation, significantly expediting the entire process.
Quality: We ensure quality at every stage by integrating human experts into the loop for quality assurance and enforce strict schema adherence.
Transparency: We provide complete and authentic information about the tools used,the quality checks performed, and deliver QA/QC reports with every dataset.
Easy Consumption: Structured data storage on an Atlas ensures easy findability and searchability, offering the flexibility of programmatic access with PollyPy or GUI access on the Polly platform.

To conclude, RNA-Seq processing involves a complex interplay of tool selection, resource management, data quality assurance, and metadata accuracy. Elucidata offers a robust and efficient solution for RNA-seq data processing, by providing researchers with the necessary tools to unlock the full potential of transcriptomic data and advance scientific inquiries.