Question: DESEQ2 is not normalizing HTSEQ counts for some samples
gravatar for sergey.yegorov
11 months ago by
sergey.yegorov0 wrote:

I have RNAseq HTSEQ count data for 3 individuals collected at 3 time points. I would like to perform count normalization across all 3 time points for each individual separately using Galaxy DESEQ2. So far I find that DESEQ2 is providing normalized counts for some samples but it outputs the original raw HTSEQ counts for others (2 out of 9 samples consistently have this issue). Has anybody encountered this before? Thanks, Sergey

ADD COMMENTlink modified 11 months ago by Jennifer Hillman Jackson25k • written 11 months ago by sergey.yegorov0

Hi there, I am dealing with the same issue with my data, one of my replicates is not normalizing in DEseq2 even though all replicates were analyzed with the same settings. I was curious if you were about to resolve this issue or could provide more information. What I've tried so far: -Remapping the original .fasta file -Doing htseq-count again from the new alignment (counts matched the first attempt) -Using DEseq2 with all replicates plus this new one; found that this replicate was still the only one not normalizing.

ADD REPLYlink written 6 months ago by kjh31810
gravatar for Jennifer Hillman Jackson
11 months ago by
United States
Jennifer Hillman Jackson25k wrote:


For your case, the experimental design may need some parameter tuning or a parameter intended to be set was missed. Double check how you set this up against the tutorials linked below to determine why the results differ between samples. I would also suggest reviewing the upstream jobs (mapper - HISAT2? and htseq_count itself) to ensure all data was processed the same way.

Galaxy tutorials for RNA-seq can be found here along with example data:

Those in the first group have been modified to work with the tools available at, for example:

And this tutorial from the GTN, also linked from the page above, contains the same basic data from the tutorial, and also explains normalization methods in detail:

Thanks! Jen, Galaxy team

ADD COMMENTlink written 11 months ago by Jennifer Hillman Jackson25k
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