Bulk RNA-Seq Analysis Demystified: Step-by-Step Tutorial Part 7 Read Alignment or Mapping by STAR
Welcome to Part 7 of our Bulk RNA-Seq Analysis series! In this tutorial, we'll explore the crucial steps of read alignment or mapping using STAR. By the end of this video, you will learn how to:
🔹 Download a reference genome
🔹 Generate genome indices using STAR
🔹 Perform read alignment with STAR
These steps are vital for precise RNA-Seq data analysis, ensuring your data is ready for downstream processing and interpretation.
Link for Original STAR publication:
https://lnkd.in/e3waNycN
Link For STAR mannual:
https://lnkd.in/etXH8fUr
Script Used
Star Indexing
STAR --runMode genomeGenerate \
--runThreadN 10 \
--genomeDir ./STAR_index/ \
--genomeFastaFiles ./Mus_musculus.GRCm39.dna.primary_assembly.fa \
--sjdbGTFfile ./Mus_musculus.GRCm39.112.gtf \
--sjdbOverhang 99
Star Alignment
STAR --runThreadN 20 \
--genomeDir ./STAR_index/ \
--readFilesIn ./trimmomatic/01_sortmerna_trimmomatic_R_1.fq ./trimmomatic/01_sortmerna_trimmomatic_R_2.fq \
--outFileNamePrefix ./star_align/01_sortmerna_trimmomatic_R_ \
--outSAMtype BAM SortedByCoordinate## Star Indexing
🔔 Don't forget to like, subscribe, and hit the bell icon to stay updated with our latest tutorials!
Disclaimer:
The information provided in this tutorial is intended for educational and instructional purposes only. The tutorial creator and platform do not assume any liability for any errors, omissions, or inaccuracies in the content. It is essential to exercise caution and follow best practices when conducting experiments and data analysis in a laboratory setting.