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:
Download the latest release from and uncompress it. # Get latest STAR source from releases wget https://github.com/alexdobin/STAR/ STAR manual 2.7.0a
High percentages (usually >70%) indicate high-quality data and successful alignment. Download STAR bin
Use the following command to download the static binary, which is the easiest to use as it has no external library dependencies: wget https://github.com chmod +x STAR Use code with caution.
Reads that map to more than one location. Once the index is ready, running the alignment
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 Use the following command to download the static
After the run, look for . This report includes critical metrics such as: