search

aakechin / NGS-PrimerPlex

NGS-PrimerPlex is a high-throughput tool for mupltiplex primer design
GNU General Public License v3.0
54 stars 21 forks source link

Definition of Primers_Score value #38

Closed alicia-hg closed 2 years ago

alicia-hg commented 2 years ago

Hi! I would like to know the definition of the Primers_Score value that is calculated for each pair of primers in all the output drafts. With which values is calculated, and how? Lower value is better? Moreover, I would like to know if this value is used in posterior steps of the pipeline Thank you so much!

aakechin commented 2 years ago

Hi @alicia-hg , the primers_score is a 'PRIMER_PAIR_PENALTY' that primer3 gives for each primer pair. Yes, lower is better. However, in posterior steps of the pipeline, it is not used. It was added in the NGS-PrimerPlex to use it later, however, this value turned out to be useless.