Following sequencing, the ribosome reads have to be mapped onto the genome. First, the adaptor sequences are clipped off using the STAR build-in clipper (or fastx). Before the ribosome read are mapped onto the genome, reads are mapped against rRNA, tRNA, snRNA and snoRNA as a filtering step. Next, the unmapped reads are then mapped on the genome, the genome and annotation files are constructed with annotation from Ensembl and the UCSC reference genome. sORFs.org uses
The STAR splice-aware mapper1,2
to perform genome-wide mapping of ribosome-protected fragments (RPFs). Next, the ribosome A-site is predicted by taking a rule-based offset from the start-site, or using
Plastid (for datasets processed using Ensembl v88 or later).
Please consult the available literature for an in depth description of the mapping procedure. Mapping statistics can be found on the datasets detail page.