Deseq2 differential expression analysis

Dear All,
I am new to galaxy
For Deseq2, should I use feature counts files as input (treated vs control)? should I include the Annotation.gff3 file as well, which I downloaded from the Gencode website?
I am using feature count files as in put and not getting gene symbols.

Thanks in advance,



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Welcome, @rizwan_rehman_rehimi

These tools only know about the annotation features that are included in the reference annotation incorporated during counting.

You might need to make changes on tool forms to access different annotation features within your files, or you might need to convert the original identifiers using a tool like AnnotateMyIDs.


You are welcome to share your data (annotation file, Featurecount’s job information/parameters) for any followup questions. For how-to, please see the banner at this forum, or here