problem in finding differentially expressed genes
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How about processing your data using a not-out-of-date DE program (e.g. deseq2, sleuth, limma), doing proper QC, and showing proper plots (e.g. MA plot, volcano plot, etc.)?
Good even sir, first of all, I am very thankfull for your reply. sir, I have mapped my data with Eucalypts Grandis as a reference genome, results showed an error after the ht-seq count command there shows 0 in the ambiguous category of the results..but when we mapped it with another genome rather than Eucalypts Grandis it shows good ambiguous in results. now I have another question it is that...is there an error with the Eucalypts Grandis reference genome or GTF file of Eucalypts Grandis