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Çılga edited this page Aug 10, 2018
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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.
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 *