After sending a DNA sample for sequencing, the resulting sequence had N's in the beginning and end of the sequence. I know the N's mean that the computer can't tell what the base pair is, but why is this?
As you accurately stated, N bases in sequence data generally means the software is unable to identify the base. N bases may appear at the beginning of the sequence result for a number of reasons. One reason would be purification of the amplified product before electrophoresis. Salts in the sample or a poor purification could leave excess dyes in the sample and appear as "dye blobs." Another reason is the software may have started analysis too soon before accurate sequence begins. Typically, quality sequence data begins 30 bases from the primer. N bases at end of the sequence simply could be the end of sequence data as stated earlier. Other reasons include hairpin loops and poly base regions that cause early termination. The best way to determine the cause is to look at the trace data.