<p>Align all reads from a sample at the same time IMO. This will give you all of the information at once, and it should not be difficult. It should be very obvious whenever there's a disagreement between reads or between reads and reference.</p>
<p>I would also recommend inspecting chromatograms directly at all sites of interest (such disagreements, insertion sites, possible errors or mutations).</p>

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2021-05-08T01:23:24.613Z
2021-05-08T01:23:24.613Z
Maximilian Press
<p>I am analyzing Sanger sequencing data to verify whether or not the correct protein coding sequence was inserted during cloning.</p>
<p>For each sample, I have both forward and reverse Sanger sequencing reads that cover the coding sequence.</p>
<p>Would it be better if I first align the forward and reverse reads to get a consensus, and then align the consensus to the reference?
Or should I just align each read directly to the reference?</p>

<phylogenetics>
Alignment to verify plasmid from forward and reverse Sanger sequencing reads
# Alignment to verify plasmid from forward and reverse Sanger sequencing reads

(Asked by: username_0 on 2021-05-07)

I am analyzing Sanger sequencing data to verify whether or not the correct protein coding sequence was inserted during cloning.

For each sample, I have both forward and reverse Sanger sequencing reads that cover the coding sequence.

Would it be better if I first align the forward and reverse reads to get a consensus, and then align the consensus to the reference?
Or should I just align each read directly to the reference?

**Tags:** phylogenetics

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## 1 answers

### Answer by username_1 on 2021-05-08. Score: 2

Align all reads from a sample at the same time IMO. This will give you all of the information at once, and it should not be difficult. It should be very obvious whenever there's a disagreement between reads or between reads and reference.

I would also recommend inspecting chromatograms directly at all sites of interest (such disagreements, insertion sites, possible errors or mutations).


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