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RSeQC

RSeQC

RSeQC tool consists of a set of tools for quality assessment of RNA-seq data. The RSeQC package includes functions for sequence quality, nucleotide composition, GC, and PCR bias, sequencing depth, strand specificity, mapped reads distribution, coverage uniformity, RNA integrity, and genomic read distribution.

Topic

Sequencing

Details

  • Operation: Data handling
  • Software interface: Command-line user interface; Suite
  • Language: Python; C
  • Operating system: Linux; Mac OS X
  • License: GNU General Public License v3
  • Cost: Free
  • Version name: -
  • Credit: The Department of Defense Prostate Cancer Program, the Cancer Prevention and Research Institute of Texas.
  • Contact: Liguo Wang wangliguo78 _at_ gmail.com | Shengqin Wang wzsqwang _at_ gmail.com | Wei Li superliwei _at_ gmail.com
  • Collection: -

Publications

Wang L, Wang S, Li W "RSeQC: quality control of RNA-seq experiments." Bioinformatics. 2012 Aug 15;28(16):2184-5. Epub 2012 Jun 27. https://doi.org/10.1093/bioinformatics/bts356
PMID: 22743226


Wang L, Nie J, Sicotte H, Li Y, Eckel-Passow JE, Dasari S, Vedell PT, Barman P, Wang L, Weinshiboum R, Jen J, Huang H, Kohli M, Kocher JP "Measure transcript integrity using RNA-seq data" BMC Bioinformatics. 2016 Feb 3;17:58. https://doi.org/10.1186/s12859-016-0922-z
PMID: 26842848
PMCID: PMC4739097


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