I have a project with both RNA-Seq and Ribo-Seq. I would like to know if it makes more sense to map them with similar parameters or should I use short-reads specific parameters for the Ribo-Seq data?
After trimming and preprocessing the Ribo-Seq data I have reads in varying lengths between 12-63, while the RNA-Seq is all 75nt long.
In the genome indexing step:
Do I need to create two different indexed genomes for the two data sets?
What would you use as a value for sjdbOverhang = ?
In the mapping step:
Does it make sense to include in the Ribo-Seq mapping also such parameters as:
thanks in advance