Cufflinks

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Application data

Biological application domain(s) RNA-Seq Alignment, RNA-Seq Quantitation, Differential Expression, Alternative Splicing, De novo transcriptome assembly, RNA-Seq
Principal bioinformatics method(s) Assembly, Differentially expressed gene identification, statistical testing
Technology Illumina, 454, Ion Torrent
Created at University of Maryland, UC Berkeley, Caltech
Maintained? Maybe
Input format(s) SAM
Output format(s) GTF
Licence Boost

Summary: Cufflinks assembles transcripts and estimates their abundances in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one.

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Links


References

  1. . 2010. Nature Biotechnology


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