quires about fpkm and log2fold change

0

Entering edit mode

4.8 years ago

Balatheskulter • 0

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.

R next-gen rna-seq • 1.0k views

ADD COMMENT • link updated 4.7 years ago by Biostar 20 • written 4.8 years ago by Balatheskulter • 0

0

Entering edit mode

What tools have you used to calculate FPKM?

ADD REPLY • link 4.8 years ago by Arup Ghosh 3.2k

0

Entering edit mode

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

ADD REPLY • link 4.8 years ago by Balatheskulter • 0

1

Entering edit mode

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