RNA Sequencing Analysis Pipeline

In this video I will explain the RNA-Sequencing Data Analysis Pipeline. RNA-Seq is an exciting and in-demand next-generation sequencing (NGS) method used for identifying genes and pathways underlying certain diseases or conditions.

RNA-Sequencing data analysis pipeline starts with the raw dataset which is in the fastq or bam file format. It contains sequence reads which are called raw reads before pre-processing. After retrieving the dataset we will perform the next step in the pipeline which is quality control.

Quality control and pre-processing of data are important for data analysis because raw data produced after sequencing must be processed so that the results should not have false positive and false negative results. It can be done with various tools for instance FASTQC, Trim Glore. Pre-processing of data not only evaluates each analysis step but also it reduces the amount of low-quality sequence reads or adaptor contaminated sequence reads.

Then comes the next step of the pipeline which is read mapping. Read mapping is important because these sequence reads have no value until they are mapped or aligned against a reference genome or assembled into a genome using de novo assembly. For that purpose we use the tool HISAT2.

Next step of the pipeline is assembly which is done by using StringTie. In assembly for the purpose of quantification we assemble the reads into a transcriptome. This quantification will help us in creating raw gene countables.

The rest of the pipeline will be discussed in the next video.

Learn BioCode’s Hands-on RNA-Sequencing with Linux & R course. This command-line based practical RNA-Seq data analysis with linux & R is absolute for beginners who have no prior experience in Linux, R or even RNA-Seq. In this course you’ll learn:

-Introduction to RNA-Seq, NGS
-In-depth Knowledge of R & Linux
-Command-line tools for RNA-Seq
-Quality Control and Trimming
-Mapping & Evaluation of Alignment
-Discovering DEGs with DESeq2, edgeR & Ballgown
-Functional Analysis with Gene Ontology & KEGG Pathways

To learn more about RNA-Sequencing DM us, we can help you get started. BioCode provides an interactive platform to learn biological programming in Python & R, bioinformatics techniques, tools, databases, and biological data analysis in a cooperative manner covering both theoretical and practical aspects of the computational biology topics. BioCode provides you with videos regarding every topic along with exercises. BioCode gives you the opportunity to learn at your pace according to your own schedule. Along with every video BioCode provides you with the transcriptions and powerpoint presentation regarding that topic. In case you have any query during the lectures, there’s a dedicated section available for you to ask questions from your tutor.

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