Difference between revisions of "MMSEQ"
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{{Bioinformatics application | {{Bioinformatics application | ||
| − | |sw summary=Pipeline and methodology for simultaneously estimating isoform expression and allelic imbalance in diploid organisms using RNA-seq data. | + | |sw summary=Pipeline and methodology for simultaneously estimating isoform expression and allelic imbalance in diploid organisms using RNA-seq data. |
| − | |bio domain=Allele-specific transcription, | + | |bio domain=Allele-specific transcription, |
| + | |maintained=Yes | ||
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== Description == | == Description == | ||
Revision as of 20:05, 25 May 2011
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| Biological application domain(s) | Allele-specific transcription |
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| Maintained? | Yes |
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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References
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