Summing the counts of duplicated genes in RNA seq data?
I have RNA seq data set for my coral samples that duplicated genes is common in the data set. I want to know, summing the counts of duplicated genes (i.e., genes with the same SYMBOL) is a valid and commonly used approach in DESeq2 and DEG analysis workflows?
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What is the origin of those genes. Are they entries with same name in GTF but different chromosomal locations (e.g. copies) or multiple transcripts from same gene?
Hi Thank you so much for your attention. These are most consistent with multiple transcripts from the same gene. I think, alternative isoforms generated from a single genomic locus. Totally I have 28059 transcripts that around 2000 of them are duplicated and totally 19544 are duplicated! Actually, the DEGs analysis without summing them was the same as I summed. And I am confused about that.
What did you use for doing the analysis?
salmonorkallistowill be perfect. Gene level analysis is generally common, so summing is probably fine but would depend on how you did the actual analysis.Thank you again! I used: QC : FastQC Alignment: STAR Counting Reads: htseq-count Differential Expression: DESeq2
Actually, I think maybe I should leave them as are, because at gene level my data look like as image I sent, with different expression levels that should be important. Right? Thanks!
Did you use a transcriptome reference or genome reference? If you are using a transcriptome reference you should use programs mentioned above. Using STAR is not appropriate in this case.
I used genome reference. So, I should leave the genes as they are in analysis, yes? Thanks