quires about fpkm and log2fold change
Hi buddies!! I have a doubt, I get different FPKM values when I use different software's, but once when I calculate log 2 fold change I get similar values for all... Is it the right method can I proceed with it.
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Balatheskulter •
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Balatheskulter •
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What tools have you used to calculate FPKM?
I have used the tuxedo pipeline and tophat -> htseq->Deseq2. both give different FPKM values with the same ratio difference between test and control, hence I get similar log2foldchange
I suggest you do not use any of these deprecated "tuxedo" tools and instead use a modern and maintained pipeline. Suggestions are in here: https://www.bioconductor.org/packages/devel/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html
thank you, let me try it out