3500 genetic analyzer low quality value

[Ghada]

Dear professor
we have a new 3500 genetic analyzer that sanger/dye terminator from applied biosystem. All amplicon have e low to medium quality value the same site 75-85 bp including the control PGEM, however the seq standard is ok. please check attached files
Any comments
regards
Ghad

[MU Core]

Ghada, you're observing the presence of "dye blobs" which is the result of poor removal of unincorporated dye terminators from the post-sequencing reaction. A common issue in dye terminator sequencing. You'll want to revisit your reaction clean-up method to see if changes can be made to optimize the method. Or, you may want to consider a different approach to reaction clean-up. Performing a google search with "removing dye blobs" will provide you with information on the topic.

[Ghada]

thank you MU core for your help.
Regards
Ghada