URL: http://www.raetschlab.org/suppl/mitie
Proper Citation: MiTie (RRID:SCR_005228)
Description: Software framework for simultaneous RNA-Seq-based Transcript Identification and Quantification in Multiple Samples. They define a likelihood function based on the negative binomial distribution, use a regularization approach to select a few transcripts collectively explaining the observed read data, and show how to find the optimal solution using Mixed Integer Programming. MiTie can a) take advantage of known transcripts, b) reconstruct and quantify transcripts simultaneously in multiple samples, as well as c) resolve the location of multi-mapping reads. It is designed for genome- and assembly-based transcriptome reconstruction.
Abbreviations: MiTie
Synonyms: MiTie: Simultaneous RNA-Seq-based Transcript Identification and Quantification in Multiple Samples
Resource Type: software resource
Keywords: c++, rna-seq, transcript
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