The article "Mapping RNA-seq Reads with STAR" by Alexander Dobin and Thomas R. Gingeras from Cold Spring Harbor Laboratory provides a comprehensive guide to using the STAR software for aligning RNA-seq reads to a reference genome. STAR is designed to handle the challenges of aligning spliced RNA sequences with high accuracy and speed, making it suitable for detecting annotated and novel splice junctions, as well as more complex RNA structures like chimeric and circular RNA. The software generates output files that are useful for various downstream analyses, including transcript/gene expression quantification, differential gene expression, and novel isoform reconstruction. The article covers several computational protocols, including the basic mapping protocol, alternate protocols for generating genome indices, 2-pass mapping, BAM output, signal visualization, chimeric alignment, transcriptomic coordinates, and integration with other tools like RSEM and Cufflinks. Each protocol details the necessary resources, input files, and command-line options to achieve specific goals. Key features of STAR include its ability to align reads of any length with moderate error rates, support for emerging sequencing technologies, and scalability. The article also provides troubleshooting tips for common issues, such as parameter errors, input file formatting, and computing resource limitations. Overall, STAR is an open-source software that can be run on Unix, Linux, or Mac OS X systems, making it accessible to a wide range of researchers.The article "Mapping RNA-seq Reads with STAR" by Alexander Dobin and Thomas R. Gingeras from Cold Spring Harbor Laboratory provides a comprehensive guide to using the STAR software for aligning RNA-seq reads to a reference genome. STAR is designed to handle the challenges of aligning spliced RNA sequences with high accuracy and speed, making it suitable for detecting annotated and novel splice junctions, as well as more complex RNA structures like chimeric and circular RNA. The software generates output files that are useful for various downstream analyses, including transcript/gene expression quantification, differential gene expression, and novel isoform reconstruction. The article covers several computational protocols, including the basic mapping protocol, alternate protocols for generating genome indices, 2-pass mapping, BAM output, signal visualization, chimeric alignment, transcriptomic coordinates, and integration with other tools like RSEM and Cufflinks. Each protocol details the necessary resources, input files, and command-line options to achieve specific goals. Key features of STAR include its ability to align reads of any length with moderate error rates, support for emerging sequencing technologies, and scalability. The article also provides troubleshooting tips for common issues, such as parameter errors, input file formatting, and computing resource limitations. Overall, STAR is an open-source software that can be run on Unix, Linux, or Mac OS X systems, making it accessible to a wide range of researchers.