I work with ribosome profiling data and I want to check the coverage of reads on the start codon.
My start is with an GRAngesList object I obtained from cdsBy(txdb, by=„tx).
In the end I want to obtain a GrangesList object with transcript id as names, and start of startcodon and stop of startcodon (+3 nts), which I then can put in the summarizeOverlaps to count features per region.
My question now is what the most efficient way of proceeding is. I though about writing an lapply function which loops through all elements in the GRangesList, searches the start of the cds (depending on strand orientation), and then built a new GRangesList object.
However, as I know R there must be an easier way to proceed. biomaRt from what I saw does not provide the genomic coordinates of the start codon. Most Ribosome profiling tools like Riboprofiling or riboseqR seem not to provide this kind of function.
Thanks for any advice!