MMSEQ
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Application data |
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| Biological application domain(s) | DNA transcription |
|---|---|
| Maintained? | Yes |
| Input format(s) | FASTQ |
| Programming language(s) | C++ |
| Software libraries | Boost, GSL, SAMtools |
| Operating system(s) | Mac OS X, Linux 64 |
Summary: Pipeline and methodology for simultaneously estimating isoform expression and allelic imbalance in diploid organisms using RNA-seq data.
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Description
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.
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