The analysis of RNA-Seq data involves several steps: quality control, read alignment, transcript assembly, and quantification. Various bioinformatics tools and algorithms are used for these tasks. For example, FastQC is commonly used for quality control, while HISAT2 and STAR are popular tools for read alignment. For transcript assembly and quantification, StringTie and Kallisto are widely used. Differential expression analysis is often performed using tools like DESeq2 and edgeR.
