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. 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. Use the following command to download the static
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 Before you can align
Before you can align reads and generate a report, you must create a genome index from your reference FASTA and GTF files.
After the run, look for . This report includes critical metrics such as: