EMSAR: estimation of transcript abundance from RNA-seq data by mappability-based segmentation and reclustering.
BACKGROUND
RNA-seq has been widely used for genome-wide expression profiling. RNA-seq data typically consists of tens of millions of short sequenced reads from different transcripts. However, due to sequence similarity among genes and among isoforms, the source of a given read is often ambiguous. Existing approaches for estimating expression levels from RNA-seq reads tend to compromise between accuracy and computational cost.


RESULTS
We introduce a new approach for quantifying transcript abundance from RNA-seq data. EMSAR (Estimation by Mappability-based Segmentation And Reclustering) groups reads according to the set of transcripts to which they are mapped and finds maximum likelihood estimates using a joint Poisson model for each optimal set of segments of transcripts. The method uses nearly all mapped reads, including those mapped to multiple genes. With an efficient transcriptome indexing based on modified suffix arrays, EMSAR minimizes the use of CPU time and memory while achieving accuracy comparable to the best existing methods.


CONCLUSIONS
EMSAR is a method for quantifying transcripts from RNA-seq data with high accuracy and low computational cost. EMSAR is available at https://github.com/parklab/emsar.
Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
Soohyun
S
Lee
Emerging Technology Center, DNA link, Seoul, South Korea.
Chae Hwa
CH
Seo
Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
Burak Han
BH
Alver
Emerging Technology Center, DNA link, Seoul, South Korea.|Ewha Womans University, Seoul, Korea.
Sanghyuk
S
Lee
Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA. peter_park@hms.harvard.edu.|Informatics Program, Boston Children's Hospital and Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA. peter_park@hms.harvard.edu.
Peter J
PJ
Park
D001483:Base Sequence; D020869:Gene Expression Profiling / Q000379:methods*; D016678:Genome / Q000235:genetics*; D020033:Protein Isoforms / Q000235:genetics*; D012313:RNA / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*; D059467:Transcriptome
D020033:Protein Isoforms; D012313:RNA