Is it necessary to trim adapters before using salmon?

[diyang1354]

If an adapter is not trimmed, will it affect the mapping rate?

[rob-p]

Hi @diyang1354,

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.