RNASEQR is a nucleotide sequence mapper/aligner and is designed specifically for RNA-seq data analysis. It takes advantage of annotated transcripts and genomic reference sequences to obtain high quality mapping/alignment results.
The functions of ERANGE are to (i) assign reads that map uniquely in the genome to their site of origin and, for reads that match equally well to several sites (‘multireads’), assign them to their most likely site(s) of origin; (ii) detect splice-crossing reads and assign them to their gene of origin; (iii) organize reads that cluster together, but do not map to an already known exon, into candida
ShortFuse is a software to identify fusions with ambiguously mapping read pairs without generating numerous spurious fusions from the many mapping locations.
RSEQtools is a suite of tools that use Mapped Read Format (MRF) for the analysis of RNA-Seq experiments. MRF was developed to address privacy concerns associated with the potential for mRNA sequence reads to identify and genetically characterise specific individuals; it is a compact data summary format that enables anonymization of confidential sequence information, while maintaining the ability to conduct subsequent functional genomics studies. RSEQtools provides a suite of modules that convert to/from MRF data and perform common tasks such as calculating gene expression values, generating signal tracks of mapped reads, and segmenting that signal into actively transcribed regions.
IQSeq is a tool for isoform quantification with RNA-seq data. Given isoform annotation and alignment of RNA-seq reads, it will use an EM algorithm to infer the most probable expression level for each isoform of a gene.
Wan L, Yan XT, Chen T and Sun FZ (2011)
RD: A Program for Statistical Estimation of Isoform Expression Levels using RNA-Seq Based on the Modeling of RNA Degradation
submitted.
CEDER is intended to implement a program for detecting differentially expressed genes (DEG) using RNA-Seq by combining significance of exons within a gene.
Wan L, Sun FZ (2011):
CEDER: Accurate detection of differentially expressed genes by combining significance of exons using RNA-Seq
(submitted to APBC2012).