Use of paired end reads by Salmon

[Max Coulter]

The question I have is regarding the use of paired end information. To what extent does the Salmon algorithm use paired end information when carrying out quantification of genes and transcripts?

We need to know whether it is worth paying extra to do PE Illumina sequencing for RNA-Seq that will be used for quantification.

Thanks for your help!

Max

[Stephen M. Mount]

Yes!

Paired end information is extremely useful, particularly when using selective alignment in the latest version of salmon. 

See https://salmon.readthedocs.io/en/latest/salmon.html