Best coverage measurements specifically for genes

Question

[DR]

Hi everyone!

I am working on a metagenomics project and I constructed a gene catalog for all the metagenomic samples. I want to identify the coverage for each of the genes in the catalog. So far, I tried Samtools depth and I used the average coverage per position in the gene as a coverage measure. The issue comes when I analyze how the coverage is distributed across the genes for different gene lengths. I observe that this stops being homogenous for larger genes and so I am looking for better measurements that may normalize the coverage estimation for this specific issue.

Thanks in advance!