User guideΒΆ
You want to generate count tables from matched Ribo- and RNA-seq data? First, you need to prepare genome indices and annotations for your organism. This has to be done once for any given reference genome and annotation. Consult How to prepare annotations.
You can estimate translation efficiency, you can find regulated Ribo-seq ORFs across conditions, with or without matched RNA-seq data, and much more. Consult How to estimate abundance, How to estimate TE or How to estimate DE.
Hint
You can use the output of Rp-Bp as input to Ribotools. In fact, Ribotools can be used with existing alignments (Ribo- and/or
RNA-seq), provided the files follow the naming convention as described in the Rp-Bp package, see
How to use existing alignment files. If using existing output or
alignment files, do not use the --overwrite option!