RSEM : RNA-Seq transcript quantification

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

 BMC Bioinformatics volume 12, Article number: 323 (2011) 

 https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-323

RNA-Seq gene expression estimation with read mapping uncertainty

Bioinformatics, Volume 26, Issue 4, 15 February 2010, Pages 493–500

 https://doi.org/10.1093/bioinformatics/btp692

 

RSEM tutorial

https://github.com/bli25broad/RSEM_tutorial