QC Analysis from Sanger sequencing
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10 days ago
davidmaimoun ▴ 50

Hello, I need to write a script to fetch qc from sanger sequencing:

signal_range, noise_range, signal_to_noise_ratio, read_length

The signal range is the the difference of the max peak and the min peak, all nucleotides together. I have a ab1 file as input.

But I don't understand why I get 9018 values for a total sequence of 755.

How could I isolate only the peaks?

My code (python):

 record = SeqIO.read(file_path, "abi")
 channels = ["DATA9", "DATA10", "DATA11", "DATA12"]
 labels = ["A", "C", "G", "T"]
 peak_data = {
    label: record.annotations["abif_raw"][channel] for label, channel in zip(labels, channels)
}
# Print Channel9 length : 9018
 print(len(record.annotations["abif_raw"][channel]))

Thank you for your help

qc ab1 sanger • 375 views
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Data channels contains the continous fluorescence signal. They're not peaks. I think peaks are in the PLOC1 but I am not sure its been a while since I worked with it.

Here is my app that I used to work on.

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Thank you I see the peaks! Is it normal to get very small peak (I got min=3, max=8000)

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See if tracy is of any use: https://github.com/gear-genomics/tracy

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Thank you for the help,

I have the peaks. I get with 'tracy' values that i also got from my code. But something doesn't make sense for me. I have a 755 sequence length, 755 different peaks. I want tot get the signal intensity range for QC. value > 1500 or < 455 not good according to my boss directive. It doesn't seem to me logic to get the of all the peaks to get the value, since I have very different peaks intensity

Somebody can help?

Thank you

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