Degenerate primers
2 answers
Also this data is from a minion device
Since we don't fully know what you are trying to do (or what your construct is supposed to look like) this may be a bit difficult to answer.
can i use alignments of sequences from ngs data before trimming to find from what locations my pcr was done?
That is what you may need to do. What is the size of the amplified product? Since not all nanopore reads will be full length you may need to work on manually editing the alignments. Hope you have a reference available, which will make this a little easier.
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