B. Howard, und S. Heber. BMC Bioinformatics, (2010)Seqmap is used as alignment tool which might be slow. Arabidopsis is used.. takes into account the non-uniformity of RNA-Seq read positions along the targeted transcripts. assumed that the set of splice variants is known; the goal is to estimate the relative expression levels of these isoforms in a mixture. Implementation The algorithm described above was implemented in Java, with matrix computations by the JAMA matrix library (available at http://math.nist.gov/javanumerics/jama/ webcite). Data analyses and simulations were also performed using the R statistical programming language (http://www.r-project.org/ webcite). Real RNA-Seq datasets For each dataset, reads were mapped to the transcriptome using the SOAP v2 alignment program 15. TAIR 8 was used to define the tested gene models. Differential splicing We first used a chi-square test of subset counts to identify genes that were differentially spliced between the two conditions. “Multireads,�? or reads that map to more than one gene, are another important problem for accurate isoform quantification..