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= | + | |bio domain=DNA transcription, |
+ | |maintained=Yes | ||
+ | |input format=FASTQ | ||
+ | |language=C++ | ||
+ | |library=Boost, GSL, SAMtools | ||
+ | |os=Mac OS X, Linux 64, | ||
}} | }} | ||
== Description == | == Description == |
Latest revision as of 18:59, 19 December 2015
Application data |
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Biological application domain(s) | DNA transcription |
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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.
Links
References
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