High percentages (usually >70%) indicate high-quality data and successful alignment.
STAR --runThreadN [threads] \ --genomeDir /path/to/index/ \ --readFilesIn read1.fastq read2.fastq \ --outFileNamePrefix SampleName_ Use code with caution. 4. Interpretation of the Report
The most direct way to obtain STAR is via its official GitHub repository. Download STAR bin
Reads that map to more than one location.
Helpful for diagnosing contamination or poor library quality. Interpretation of the Report The most direct way
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: including the file
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