Question: deseq2 pre filter rna seq
0
gravatar for badribio
4 months ago by
badribio0
badribio0 wrote:

I see more and more papers these days that use a read cut off before deseq2 analysis, I wonder what is the rational and/or how do they arrive at how many reads is a right number..for example from one of the papers DESeq2 was applied to genes having more than 20 reads in half the number of samples ^ this study had n=8 4wt and 4ko. i could not comprehend how did they arrive at the number 20, even if they did what if the differences are genotype driven more over DESeq2 has independent filtering which takes care of low counts no?

Is there a way one can plot counts and determine what is a right threshold for pre filtering

Thanks

rnaseq deseq2 • 177 views
ADD COMMENTlink modified 4 months ago by zefrieira0 • written 4 months ago by badribio0

You'll likely get better answers if you employ some punctuation.

ADD REPLYlink written 4 months ago by swbarnes2340

excuse me, hope i did ok this time.

ADD REPLYlink written 4 months ago by badribio0
Answer: deseq2 pre filter rna seq
0
gravatar for zefrieira
4 months ago by
zefrieira0
zefrieira0 wrote:

DESeq2 filters genes based on their counts. Read the independent filtering section of the documentation.

ADD COMMENTlink written 4 months ago by zefrieira0

Correct. We do sometime perform minimal pre-filtering. Mostly this is to reduce unnecessary computation, whereas the independent filtering (or better yet, IHW) is for increasing power. There is no need to run DESeq2 for bulk RNA-seq on genes where only one or two samples have a single digit count and the rest have all 0's.

ADD REPLYlink written 4 months ago by Michael Love26k
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