distribution of read-count per gene for results by HTSeq-count

Question

[Pei]

Hi all:

After running HTseq-count to get read counts for each gene, typically how many counts would you expect for a gene?

In my result for Drosophila, the median of read count per sample is only ~1.

Do you think my result is reasonable?

Thanks in advance!

Answer 1

[Devon Ryan]

There's no single value that one should expect, it's entirely dependent upon (A) the sequencing depth and (B) the cell type. In general, I would expect the median to be quite low.