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Can anyone confirm if default fold change in cuffdiff is 2? how can I reduce this to 1.5?
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As far as I know there is no fold change cutoff applied by cuffdiff
Nothing here about it
Why do you think there is a cutoff applied?
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Hi Jeales
thanks for your reply. I thought so as well. however, some genes that were 1.5-1.8 fold expressed are missing in the final list of significantly differentially expressed genes. also, I could only see -1.5 and 1.5 as lowest log2 values for DE.Comment
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Which output file are you looking at?
Also how many lines does it contain and is it the correct number? (i.e the number of genes/transcripts in the gtf)
All log 2 fold changes should be reported whether they are significant or not
Also if you're just looking at a list of significant results, then broadly speaking, results with smaller fold changes are less likely to be significant, and this might be why you aren't seeing any fold changes nearer to zeroComment
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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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