Question: DESEQ2 is not normalizing HTSEQ counts for some samples
gravatar for sergey.yegorov
5 weeks 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 5 weeks ago by Jennifer Hillman Jackson23k • written 5 weeks ago by sergey.yegorov0
gravatar for Jennifer Hillman Jackson
5 weeks ago by
United States
Jennifer Hillman Jackson23k 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 5 weeks ago by Jennifer Hillman Jackson23k
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