Hi community,
the latest cufflinks release (2.2.0) comes with two novel tools, cuffquant and cuffnorm. The latter can be used to generate expression and count tables at the level of transcripts, primary transcripts and genes, that are normalized for library size.
I was wondering whether these normalized counts can be used with one of the 'count-based' methods like DESeq/DEXSeq/edgeR, circumventing their normalization methods.
In other words, can I use e.g. the DESeq nbinomTest() function with these cuffnorm-generated data?
Thanks.
the latest cufflinks release (2.2.0) comes with two novel tools, cuffquant and cuffnorm. The latter can be used to generate expression and count tables at the level of transcripts, primary transcripts and genes, that are normalized for library size.
I was wondering whether these normalized counts can be used with one of the 'count-based' methods like DESeq/DEXSeq/edgeR, circumventing their normalization methods.
In other words, can I use e.g. the DESeq nbinomTest() function with these cuffnorm-generated data?
Thanks.
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