"RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. " "The RSEM package provides an user-friendly interface, supports threads for parallel computation " "of the EM algorithm, single-end and paired-end read data, quality scores, variable-length reads " "and RSPD estimation. In addition, it provides posterior mean and 95% credibility interval " "estimates for expression levels. For visualization, It can generate BAM and Wiggle files in both " "transcript-coordinate and genomic-coordinate. Genomic-coordinate files can be visualized by both " "UCSC Genome browser and Broad Institute's Integrative Genomics Viewer (IGV). Transcript-coordinate " "files can be visualized by IGV. RSEM also has its own scripts to generate transcript read depth " "plots in pdf format. The unique feature of RSEM is, the read depth plots can be stacked, with read " "depth contributed to unique reads shown in black and contributed to multi-reads shown in red. In " "addition, models learned from data can also be visualized. Last but not least, RSEM contains a " "simulator."