Hi, how can I use rtracklayer to create a file contains ensembl id,gene id, read counts, chr number.. etc. I have count matrix from htseq-count and human gff file but somehow I couldnt understand rtracklayer Thx

You don't use rtracklayer for that sort of thing. If you want to annotate your data, you can use either biomaRt or one of Johannes Ranier's EnsDb packages, depending on your species.