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Welcome to the RNA-seq-Tutorial wiki!

In this wiki, I will explain a very basic tutorial for my RNA-seq analysis pipeline starting from gathering FASTQ files from ENA repositories to data visualization including knowledge about next generation sequence, file formats, quality checks, reference genomes, gene annotation, expression analysis, differential expression analysis.

TABLE OF CONTENTS

Next Generation Sequencing

File Formats and Types - - fastq - Reference Genome(s) - BAM/SAM - Annotations

Pre-alignment/Post-alignment Quality Check -fastQC* -Adapter Trim -fastq -RSeQC

Alignment -bowtie -tophat / tophat2* -STAR -HISAT2

Feature Counts

Expression Analysis

Differential Expression Analysis -DESeq / DESeq2 *