STAR is a high-accuracy, fast RNA-seq read aligner that maps reads to a reference genome. It can detect annotated and novel splice junctions, as well as complex RNA structures like chimeric and circular RNA. STAR aligns spliced sequences with moderate error rates, making it scalable for emerging sequencing technologies. It generates output files for downstream analyses such as transcript/gene expression quantification, differential gene expression, and novel isoform reconstruction. The Basic Protocol describes regular mapping using a real RNA-seq dataset. Alternate Protocols cover various mapping strategies, including 2-pass mapping for novel junctions, generating unsorted and coordinate-sorted BAM files, and creating signal files for visualization in genome browsers. STAR is open-source and runs on Unix, Linux, or Mac OS X systems. It requires genome indices, which can be generated or downloaded. The protocols also describe how to map RNA-seq reads, generate chimeric alignments, output alignments in transcriptomic coordinates, and use RSEM or Cufflinks for transcript quantification. STAR is recommended for use with the latest release, and its performance can be optimized by adjusting parameters and using multiple threads. The software is widely used in RNA-seq analysis for its accuracy and efficiency.STAR is a high-accuracy, fast RNA-seq read aligner that maps reads to a reference genome. It can detect annotated and novel splice junctions, as well as complex RNA structures like chimeric and circular RNA. STAR aligns spliced sequences with moderate error rates, making it scalable for emerging sequencing technologies. It generates output files for downstream analyses such as transcript/gene expression quantification, differential gene expression, and novel isoform reconstruction. The Basic Protocol describes regular mapping using a real RNA-seq dataset. Alternate Protocols cover various mapping strategies, including 2-pass mapping for novel junctions, generating unsorted and coordinate-sorted BAM files, and creating signal files for visualization in genome browsers. STAR is open-source and runs on Unix, Linux, or Mac OS X systems. It requires genome indices, which can be generated or downloaded. The protocols also describe how to map RNA-seq reads, generate chimeric alignments, output alignments in transcriptomic coordinates, and use RSEM or Cufflinks for transcript quantification. STAR is recommended for use with the latest release, and its performance can be optimized by adjusting parameters and using multiple threads. The software is widely used in RNA-seq analysis for its accuracy and efficiency.