Cufflinks
Application data |
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Biological application domain(s) | RNA-Seq Alignment, RNA-Seq Quantitation, Differential Expression, Alternative Splicing, De novo transcriptome assembly, RNA-Seq |
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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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