DGE analyses after expressing a construct - prior removal of construct-mapping reads?

Question

[ella]

Dear DGE experts, I am trying to analyze DGE of my cells (human cell culture) that express different constructs. For that purpose, I am mostly following the https://hbctraining.github.io/DGE_workshop_salmon_online workshop (which I really appreciate!!). Going through the different steps and now preparing my own data, I was wondering, if reads that cover the foreign construct´s transcript (plant gene, no native gene) should be removed prior to Salmon quantification; or if Salmon can cope with it. For variant calling, I did remove reads, that match my OE-plasmid, via bbduk.sh (BBtools suite) prior to mapping. I am looking forward to your suggestions! Thanks a lot in advance, Ella