Being new to bulk RNA-seq analysis I have the following question: is it necessary to trim adapters from RNA-seq data before mapping with Salmon, or is this method robust to the presence of adapter sequences?
It is recommended to do adapter trimming prior to mapping and
quantification (standard practices actually involve adapter and light
quality trimming of reads). Adapter contamination could affect the
mapping rate, especially if selective-alignment, which is recommended,
is being used.