Please help to understand the concept of the sentence about cufflinks

Question

[seta]

Hi all,

I came across with this sentence about cufflinks: "When it is enabled, Cufflinks learns from the data what sequences were selected for, and re-estimates the abundances with a new likelihood function that takes the sequence-specific bias into account".

Could you please help me out to find out the concept and meaning the sentence?

Thanks

Answer 1

[Kevin Blighe]

You omitted the most important part of the quote, i.e., the sentence before it:

"Using fragment bias correction is recommended. When it is enabled, Cufflinks ... "

[source: RNA-seq Data Analysis: A Practical Approach]

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I'm going to give you the quick answer and tell you to go read the published manuscript on this specific topic by the original authors of Cufflinks: Improving RNA-Seq expression estimates by correcting for fragment bias. From what I can see, it allows Cufflinks to improve expression estimates by performing further adjustments based on differences in library sizes across your samples. EdgeR and DESeq2 also adjust for these effects through the estimation of size factors.

[seta]

Thank you, I got it.