featureCounts results has many psedugenes(ENSG***) together with genes

Question

[dew]

Dear all,

Do you know how to generate the results to all genes(-t gene already used)?

featureCounts -T 10 -s 2 -p -t gene  -a gencode.v40.primary_assembly.annotation.gtf -o gene_count.txt -g gene_name *bam

Answer 1

[iraun]

What is the issue? featureCounts will generate counts for the genes you are providing in your GTF (regardless of being genes or pseudogenes). If you don't want to generate counts for the pseudogenes you can remove them from the GTF or from the output counts file from featureCounts.

[dew]

Thanks a lot!

So should the pseudogenes be used in the downstream DEGs finding? Thanks! Best!

[iraun]

No problem :).

I am afraid that I can't answer to that question. It depends on your hypothesis and experiment. Are you interested in the expression patterns of pseudogenes? Having differentially expressed pseudogenes is something that you are looking for in your experimental design?

[dew]

Thanks! Got it. Thank you very much!Best!