Hi Everyone

I have a question related to previous procedures to do Differential Gene Expression (DEG) by using DESeq2. I have counts for 2 conditions each one with 3 replicates. After I did the DEG, I realized that are duplicated genes in the final result, because when I did the count with HTSeq I considered gene id. Thus the count considers different transcripts for the same gene when I performed the analysis.

For instance

Gene ID        Count        Gene Name

A               10            KDR
B               12            KDR

I think that I should join these counts, since they came from the same gene, but I do not have certain of this. Thus I will have 22 read count for this gene KDR in a file, and I will do the analysis considering 22 reads count for this gene intead of do the DEG for A and for B separately.

My question is: Should I join the count from different transcripts that fall in the same gene to follow the DEG analysis? If no, why?

I tried to find an answer in the forums, but I did not get one so far. Sorry if this is a basic question, I just started to do this type of analysis.

Thanks in advance for your supporting.

You need to know how the counts were generated. You can't just add them together without knowing this.