STAR --runThreadN [threads] \ --genomeDir /path/to/index/ \ --readFilesIn read1.fastq read2.fastq \ --outFileNamePrefix SampleName_ Use code with caution. 4. Interpretation of the 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:
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
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
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
Helpful for diagnosing contamination or poor library quality.
Reads that map to more than one location.
Download Star Bin Apr 2026
STAR --runThreadN [threads] \ --genomeDir /path/to/index/ \ --readFilesIn read1.fastq read2.fastq \ --outFileNamePrefix SampleName_ Use code with caution. 4. Interpretation of the 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: Download STAR bin
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 Command Example: For visualizing multiple STAR reports at
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 Generate a Genome Index STAR --runThreadN [threads] \
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
Helpful for diagnosing contamination or poor library quality.
Reads that map to more than one location.