RNA Seq Analysis | Mapping Genome Reads with STAR Aligner and visualizing with IGV - Episode 1

This bioinformatics tutorial shows you how to map rna-seq reads to a reference sequence using STAR aligner tool. After mapping we check the mapping statistics and inspect the bam file using IGV(Integrated Genome Viewer)
Scripts for this tutorial:   / 83914361  

RNA Seq Analysis with DESEq2:   • How I analyze RNA Seq Gene Expression...  
RNA Seq Analysis Tutorials:   • RNA Seq Analysis Tutorials  


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Materials
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Original Tutorial
https://training.galaxyproject.org/tr...

STAR Documentation
github: https://github.com/alexdobin/STAR
manual: https://github.com/alexdobin/STAR/blo...


Dataset
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FASTQ
forward reads: https://zenodo.org/record/4541751/fil...

reverse reads: https://zenodo.org/record/4541751/fil...

Reference sequence
fasta: http://hgdownload.soe.ucsc.edu/golden...
gtf: https://zenodo.org/record/4541751/fil...



Install Tools
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Anaconda
Linux    • Install , Configure and Run Anaconda ...  
MacOS    • Install, Configure and Run Anaconda i...   - GUI Installer
   • Install, Configure and Run Anaconda i...   - Command line installer

STAR
anaconda:    • STAR RNA Seq Download and Install | A...  
binaries:   • STAR RNA Seq Download and Install | B...  
compile from source:    • STAR RNA Seq Download and Install | C...  



Chapters
00:00 Intro
01:22 PC Requirements
02:40 Install Tools using conda
02:52 Add conda channels
03:26 Create environment and install tools
04:41 Activate the environment
04:51 Create a working directory
05:03 Create a directory to store the example data
05:25 Get the download links for the fastq files
06:45 Download the example data(fastq files)
08:46 Move the fastq files to another directory
09:26 Get the download links for the reference sequence
14:22 Quality Control
14:28 Run fastqc
16:04 Aggregate fastqc report using multiqc
18:22 Inspect the reports
22:04 Mapping reads
22:44 Index the reference sequence
28:00 Map reads using STAR
32:10 Examine the STAR output
33:34 Get the mapping statistics
36:42 Inspect the bam file.

Mapping RNA-Seq Reads with STAR Aligner and visualizing with IGV - Episode 1


Commands used

conda commands
conda create
conda install
conda env
conda activate
conda deactivate
STAR aligner commands
STAR
samtools command
samtools view
samtools index
IGV
Linux commands
cd
pwd
cat
ls
chmod +x

wget
star
fastq
multiqc

STAR Aligner Tutorial

bioinformatics
rna seq

#bioinformatics #bioinformática #bioinformaticsforbeginners #linuxforbeginners #linuxforbeginners