First of all, I fucking HATE dealing with sequencing. It's tedious, it's boring and it takes time away from actual bench work.
At my old institution all the sequencing was done at a core facility and rarely did I get anything back that wasn't pristine. There is not core facility at my new institution, so I am using a new company and I am NOT impressed.
Sure, it could be the plasmids I sent them, but I seriously doubt it. Here's why:
I checked the concentration and purity before sending the plasmids off and they were all very good.
I am using vector-specific primers that are provided by the sequencing facility and I get the following results:
gives sequence results ranging from beautiful to tolerable.
Primer 2: (same template as primer 1)
gives sequence ranging from 300 nt reads (300?!?!?) to 800 N's with a few random A's T's C's and G's dispersed throughout.
Good and bad sequence from each primer do not correlate with the template. If the worst sequence from each primer came from the same template, then I would assume the template that was the problem, but considering it did not correlate...
I'm taking a break before I blow a gasket.