I have sanger sequences (abi format) with other degenerative bases and i would like to set a phred score which will convert the bases below that quality value to N. How can I do this please?
If you have access to the computer that runs the sequencer then in the sequencing analysis software you can change many parameters and make a re analysis of your sequencing run show and annotate either more or fewer peaks depending on the level of sensitivity that you set
I would recommend the software SnapGene. It has many useful features for analyzing Sanger sequencing data and more. You can manually edit base calls and set quality cut-off parameters. I tried several other applications and this one was the most useful for working with and aligning Sanger sequencing data. It is somewhat costly, but has a free trial version.