can't remove primer using mapping file

[codechenx]

I discovered that Lotus2 cannot delete the primer when I specify the primer sequence using a mapping file, but it works correctly when I specify the primer sequence by command line.

[hildebra]

Hey Stephen, the deletion of primers should normally be controlled in the sdm_XX_opt.txt. Was teh problem solved now?

[codechenx]

thanks for your rely, I found that the forwardprimer and reverseprimer is switched in my sequencing data.