STRAND INFORMATION

[rolibudhwar]

How NGS primerplex tool is looking into the strand information for primer design?? I am not able to finf any parameter where we need to mention the strand information

[aakechin]

@rolibudhwar NGS-PrimerPlex makes one primer for + strand (on the left of sequence) and another one for - strand (on the right of sequence) relatively to the reference sequence that was defined by user. When only one primer (left or right) should be designed, it can be defined in the regions file. There is a column "type of primers (left - L, right -R or both -B, optional)" described in the Manual. It can be L to make only left primer (for + strand), R to make only the right primer (for - strand) or B to make both primers (by default).
Of course, you can use reverse complement sequence of the reference sequence (e.g. some gene). In this case left primer will by at + strand relatively to the used sequence, and the right primer will be at - strand.

[rolibudhwar]

@aakechin Thanks for your prompt reply. I have more query regarding usage of multiple Reference database. Can we use this tool to validate the primers(output of NGSprimerplax) using other references as well(eg. bacteria, fungi etac)??