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Text replace - "Allele-specific transcription" to "DNA transcription"
{{Bioinformatics application
|sw summary=Pipeline and methodology for simultaneously estimating isoform expression and allelic imbalance in diploid organisms using RNA-seq data. |bio domain=Allele-specific DNA transcription,|maintained=Yes|input format=FASTQ|language=C++|library=Boost, GSL, SAMtools|os=Mac OS X, Linux 64,
}}
== Description ==
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We present a novel pipeline and methodology for simultaneously estimating isoform expression and allelic imbalance in diploid organisms using RNA-seq data. We achieve this by modeling the expression of haplotype-specific isoforms. If unknown, the two parental isoform sequences can be individually reconstructed. A new statistical method, MMSEQ, deconvolves the mapping of reads to multiple transcripts (isoforms or haplotype-specific isoforms). Our software can take into account non-uniform read generation and works with paired-end reads.