The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
Mapping RNA‐seq Reads with STAR
Open accessAbstract
Mapping of large sets of high‐throughput sequencing reads to a reference genome is one of the foundational steps in RNA‐seq data analysis. The STAR software package performs this task with high levels of accuracy and speed. In addition to detecting annotated and novel splice junctions, STAR is capable of discovering more complex RNA sequence arrangements, such as chimeric and circular RNA. STAR can align spliced sequences of any length with moderate error rates, providing scalability for emerging sequencing technologies. STAR generates output files that can be used for many downstream analyses such as transcript/gene expression quantification, differential gene expression, novel isoform reconstruction, and signal visualization. In this unit, we describe computational protocols that produce various output files, use different RNA‐seq datatypes, and utilize different mapping strategies. STAR is open source software that can be run on Unix, Linux, or Mac OS X systems. © 2015 by John Wiley & Sons, Inc.
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Cites
The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041
STAR: ultrafast universal RNA-seq aligner
Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., & Gingeras, T. R. (2013) · Bioinformatics · doi:10.1093/bioinformatics/bts635 · Cited by 51,709
Self-citationRSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
Li, B., & Dewey, C. N. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-323 · Cited by 22,179
Trapnell, C., Williams, B. A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M. J., Salzberg, S. L., Wold, B. J., & Pachter, L. (2010) · Nature Biotechnology · doi:10.1038/nbt.1621 · Cited by 15,556
Cited by
Haas, B. J., Dobin, A., Li, B., Stransky, N., Pochet, N., & Regev, A. (2019) · Genome biology · doi:10.1186/s13059-019-1842-9 · Cited by 646
Self-citationAn ultra high-throughput method for single-cell joint analysis of open chromatin and transcriptome
Zhu, C., Yu, M., Huang, H., Juric, I., Abnousi, A., Hu, R., Lucero, J., Behrens, M. M., Hu, M., & Ren, B. (2019) · Nature Structural & Molecular Biology · doi:10.1038/s41594-019-0323-x · Cited by 344
Ni, J., Wang, X., Stojanovic, A., Zhang, Q., Wincher, M., Bühler, L., Arnold, A., Correia, M. P., Winkler, M., Koch, P.-S., et al. (2020) · Immunity · doi:10.1016/j.immuni.2020.05.001 · Cited by 324
Social status alters immune regulation and response to infection in macaques
Snyder-Mackler, N., Sanz, J., Kohn, J. N., Brinkworth, J. F., Morrow, S., Shaver, A. O., Grenier, J.-C., Pique-Regi, R., Johnson, Z. P., Wilson, M. E., et al. (2016) · Science · doi:10.1126/science.aah3580 · Cited by 318
Joint profiling of histone modifications and transcriptome in single cells from mouse brain
Zhu, C., Zhang, Y., Li, Y. E., Lucero, J., Behrens, M. M., & Ren, B. (2021) · Nature Methods · doi:10.1038/s41592-021-01060-3 · Cited by 301
Metadata
- Authors
- Dobin, A., & Gingeras, T. R.
- Venue
- Current Protocols in Bioinformatics
- Publisher
- Wiley
- Published
- 2015-09
- Volume
- 51
- Issue
- 1
- Pages
- 11.14.1-11.14.19
- ISSN
- 1934-3396 (ISSN-L)
- 1934-340X
- OpenAlex
- W2136170412
- Cited by
- 1,294
- References
- 4
- FWCI
- 14.54
- Type
- journal article
- Language
- en
- Open access
- green
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