I have an RNA-seq (RPFl Ribosomal Profiling) experiment where I want to focus my analysis on reads mapping to CDS of the human genome, but not the first 15 codons (i.e. first 45bp after ATG start codon).
For this I am trying to build a bed file with coordinates of all CDS and then remove the first 45bp after ATG. There are a lot of issues doing this manually, as for a lot of genes, the first CDS features in a GTF file is shorter than 45bp.
Is there a tool that can do this easily? Thanks.