For visualizing multiple STAR reports at once, many researchers use MultiQC , which can aggregate these .final.out files into a single, interactive HTML report. alexdobin/STAR: RNA-seq aligner - GitHub

STAR --runThreadN [threads] \ --genomeDir /path/to/index/ \ --readFilesIn read1.fastq read2.fastq \ --outFileNamePrefix SampleName_ Use code with caution. 4. Interpretation of the Report

STAR --runThreadN [threads] \ --runMode genomeGenerate \ --genomeDir /path/to/index/ \ --genomeFastaFiles /path/to/genome.fasta \ --sjdbGTFfile /path/to/annotation.gtf Use code with caution. 3. Run Alignment and Generate Report

Once the index is ready, running the alignment will automatically generate several report files, including the file, which serves as the primary alignment summary report. Command Example:

Before you can align reads and generate a report, you must create a genome index from your reference FASTA and GTF files.

High percentages (usually >70%) indicate high-quality data and successful alignment.

Helpful for diagnosing contamination or poor library quality.

If you use Anaconda or Miniconda, you can install it through the Bioconda channel : conda install -c bioconda star Use code with caution. 2. Generate a Genome Index