RNASeq Highly expressed genes in single sample

Question

[rob.costa1234]

I have to find highly expressed genes in one sample, I can do read count and find out which genes have top 100 Read counts. Can I include and kind of statistics in the list or any other better way of identifying top 100 genes.

Answer 1

[h.mon]

Read count is a terrible way of identifying highly expressed genes, as longer genes will have (on average) higher counts and be identified as "highly expressed" as a side effect. A better measure is TPM.

[venu]

@h.mon, do you think removing house keeping genes and taking top genes with high TPMs makes sense? As house keeping genes tend to have high TPMs without contributing to the phenotype/condition.

[h.mon]

I don't think so, "house keeping" genes are somewhat relative to tissue, cell line or whatever, and OP has only one sample. I was just answering his question, but in fact, I am not sure how best explore his data, or even if it is worth deeply exploring his data - but I have a "comparative" mindset.