Bulk RNA Seq Analysis Demystfied: Step by Step Tutorial Part 8
Welcome to Part 8 of our Bulk RNA-Seq Analysis series! In this tutorial, we will delve into the essential process of counting features, such as genes or exons, using FeatureCounts. By the end of this video, you will learn how to:
🔹 Install FeatureCounts and its dependencies
🔹 Prepare your aligned BAM files
🔹 Count features with FeatureCounts
🔹 Interpret the output files for downstream analysis
Feature counting is a critical step in RNA-Seq data analysis, providing the foundation for differential expression analysis and further insights into gene expression.
FEATURE COUNTS of STAR .bam
featureCounts -T 32 -a /home/shashi/rnaseq/Mus_musculus.GRCm39.112.gtf -o ./star_count/gene_counts.txt -p -B -C \
./star_align/01_sortmerna_trimmomatic_R_Aligned.sortedByCoord.out.bam \
./star_align/02_sortmerna_trimmomatic_R_Aligned.sortedByCoord.out.bam \
./star_align/03_sortmerna_trimmomatic_R_Aligned.sortedByCoord.out.bam \
./star_align/04_sortmerna_trimmomatic_R_Aligned.sortedByCoord.out.bam \
##FEATURE COUNTS OF HISAT2 .BAM
featureCounts -T 32 -a /home/shashi/rnaseq/Mus_musculus.GRCm39.112.gtf -o ./hisat2_count/gene_counts.txt -p -B -C \
./hisat2_bam_file/01_R_trimmomatic_sortmerna_sorted_bam \
./hisat2_bam_file/02_R_trimmomatic_sortmerna_sorted_bam \
./hisat2_bam_file/03_R_trimmomatic_sortmerna_sorted_bam \
./hisat2_bam_file/04_R_trimmomatic_sortmerna_sorted_bam \
🔗 Useful Links:
Original STAR publication: Link
STAR Manual: Link
FeatureCounts Documentation: [Include a link to FeatureCounts documentation or a relevant resource if available
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