Recently I need to do some analysis about ribosomal profiling data. A lot of papers recommended to filter rRNA sequences before mapping to genome. So which way is better? Using rRNA database or only use your organism annotation file(GenBank)? It seems that many people use this website database: https://www.arb-silva.de/download/arb-files/
For genbank method, I plan to download files from ensembl: ftp://ftp.ensembl.org/pub/release-79/genbank/danio_rerio/ and then use biopython to pull out all rRNA related sequences.
What is the normal way to get rid of rRNA in ribosomal profiling data analysis? Any suggestion is welcome!