What is RNA pipeline?

[Mehreen A]

What is meant by pipeline? and

What is RNA pipeline?

[Fazil Hussein]

A pipeline is a series of connected tubes for transporting gas, oil, or water, usually over long distances. In biology research, this word is used meaning workflow of specific complex experimentation.

What is RNA pipeline? answered by Bard:

An RNA pipeline is essentially a series of computational steps used to analyze data generated from RNA sequencing (RNA-seq) experiments. These experiments measure the abundance of different RNA molecules in a biological sample, providing valuable insights into gene expression, alternative splicing, and other cellular processes. However, raw RNA-seq data is complex and needs processing before it can be meaningfully interpreted. That’s where the RNA pipeline comes in.

Here’s a simplified breakdown of a typical RNA pipeline:

1. Input: The pipeline starts with raw RNA-seq data, usually in the form of FASTQ files containing millions of short DNA sequences representing RNA fragments.

2. Quality Control (QC): The first step is to assess the quality of the data. This involves checking for sequencing errors, adapter contamination, and other potential issues that could affect downstream analysis.

3. Preprocessing: This step often includes adapter trimming, where low-quality sequences and adapter sequences are removed to improve data quality.

4. Alignment: Here, the RNA sequences are aligned to a reference genome or transcriptome. This allows researchers to identify where the RNA originated from and quantify its abundance in different regions. Different alignment algorithms like STAR, HiSAT2, and Salmon are used depending on the research question.

5. Quantification: After alignment, the number of RNA sequences aligning to each gene or transcript is counted. This provides a measure of gene expression levels. Tools like RSEM and FeatureCounts are commonly used for this step.

6. Downstream Analysis: This involves interpreting the gene expression data and drawing biological conclusions. This may involve differential expression analysis, identifying differentially expressed genes between different conditions, functional enrichment analysis, understanding the biological functions of differentially expressed genes, and pathway analysis, tracing the interaction between genes involved in specific biological processes.

7. Output: The final output of the pipeline can be various depending on the analysis performed. It can include gene expression matrices, differentially expressed gene lists, functional enrichment results, and pathway diagrams.

Important points to remember:

The specific tools and steps involved in an RNA pipeline may vary depending on the research question, organism, and desired level of detail.
Building and running an RNA pipeline requires bioinformatics expertise and computational resources.
Several pre-built pipelines like nf-core/rnaseq are available, simplifying the analysis for researchers with less bioinformatics experience.

 

[C Archer]

A pipeline generally refers to a series of processes or stages involved in a particular task. In different contexts, it can have different meanings:

1. In the context of infrastructure, a pipeline is a long pipe, typically underground, for conveying substances like oil, gas, etc.
2. In business or information systems, a pipeline refers to a channel or system supplying goods or information.
3. In computer science, a pipeline is a linear sequence of specialized modules used for completion of a task.

An RNA pipeline, on the other hand, is a specific type of bioinformatics pipeline used in the analysis of RNA sequencing (RNA-seq) data. RNA-seq is a technique that examines the quantity and sequences of RNA in a sample using next-generation sequencing (NGS). The RNA pipeline includes several steps such as experimental design, quality control, read alignment, quantification of gene and transcript levels, visualization, differential gene expression, alternative splicing, functional analysis, gene fusion detection, and expression quantitative trait loci (eQTL) mapping. The specific steps and tools used can vary depending on the specific goals of the research.

Source: Conversation with Bing, 2/1/2024

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