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.
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Nucleic Acids Res. 2012 Mar;40(6):e42. Epub 2011 Dec 22.
RNASEQR–a streamlined and accurate RNA-seq sequence analysis program.
Chen LY, Wei KC, Huang AC, Wang K, Huang CY, Yi D, Tang CY, Galas DJ, Hood LE.