Do you think that pseudogenes masking for short-reads mapping is sensible? I'm analysing ribosome profiling data that are about 25-32 nt long and even after standard pre-alignment to rRNA region I still see some multi mapping that maybe could be diminished if pseudogenes regions were hard-masked in the reference genome. For example, in this paper pseudogenes masking for ribosomal proteins has changed alignment substantially.
On the other hand as ~ 15% of pseudogenes is estimated to be transcribed, such masking could potentially introduce serious bias in quantification of those genes. What is your experience?