Adapter trimming before mapping with Salmon

Question

[justinjacobse]

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?

Answer 1

[igor]

From their GitHub issues:

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.

[Dave Carlson]

To add to this, if you're worried about how long it will take to trim adaptors for a large number of samples, you may want to check out fastp. It's a very fast, "one-stop-shop" QC program that will trim adaptors, filter and/or trim reads based on quality scores, remove PCR duplicates, and provide before-and-after QC plots.

[igor]

I use Trimmomatic and the trimming takes longer than the alignment/quantification. I am not in a rush, but I do find that ironic.

[justinjacobse]

Great, thanks for answer and the additional suggestions.