Difference between revisions of "What does Cuffdiff do?"
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Where we compare the abundances of 2 samples and tell us which RNA reads are different. Ultimately gives us differential expression. | Where we compare the abundances of 2 samples and tell us which RNA reads are different. Ultimately gives us differential expression. | ||
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References: | References: | ||
Trapnell C. et al., 2010. Transcript assembly and quantification by RNA-Seq revels annotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 28(5):511-515. doi:10.1038/nbt.1621 | Trapnell C. et al., 2010. Transcript assembly and quantification by RNA-Seq revels annotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 28(5):511-515. doi:10.1038/nbt.1621 | ||
Latest revision as of 16:01, 6 February 2018
The cutdiff function finds any significant changes in transcript expression, splicing, and promoter use (Trapnell et al., 2010). Cuttdiff is an algorithm for transcript assembly that uses a statistical model to produce estimates of isoforms (functionally similar proteins with different amino acids) abundances.
Where we compare the abundances of 2 samples and tell us which RNA reads are different. Ultimately gives us differential expression.
References:
Trapnell C. et al., 2010. Transcript assembly and quantification by RNA-Seq revels annotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 28(5):511-515. doi:10.1038/nbt.1621
