density of reads that mapped to the specific gene

Question

[alirezamomeni707]

I have RNA-seq data and want to get the density of reads that mapped to the specific tRNA. do you know how to do that?

[WouterDeCoster]

Density? Do you mean counting the reads overlapping a gene?

[alirezamomeni707]

yes. and then I would make a density plot.

[WouterDeCoster]

For counting reads you can use tools such as featureCounts and htseq-count.