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sequencing trace question


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#1 claritylight

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Posted 21 September 2010 - 05:01 AM

Can anyone please tell me what is going on between 75-80bp and ~120bp? It is seen in both the forward and reverse traces, and the rest of the trace is clean except for these odd-looking peaks. I know what is going on between ~120bp could be a mutation, but I don't know what could cause the large peaks between 75-80bp. Any ideas would be helpful

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Edited by claritylight, 21 September 2010 - 05:02 AM.


#2 phage434

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Posted 21 September 2010 - 06:21 AM

That is a classic "dye blob" which occurs about exactly where this one does in many sequencing runs. The large peaks are from inadequate removal of labeled dNTPs during sequencing cleanup. If you are doing automatic processing of sequence data, they really need to be fixed. If you are looking at them by hand (which I'm guessing you are) then you can ignore them and read the trace file. The small peaks are the correct reads, and in regions where there is no small peak there is a base of the color of the broad dye blob. Your sequence is quite readable, if you follow those simple rules.

If I read the trace file, that sequence reads
tccttgtggctgcgga...




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