QC Analysis from Sanger sequencing
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
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davidmaimoun •
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Data channels contains the continous fluorescence signal. They're not peaks. I think peaks are in the
PLOC1but I am not sure its been a while since I worked with it.Here is my app that I used to work on.
Thank you I see the peaks! Is it normal to get very small peak (I got min=3, max=8000)
See if
tracyis of any use: https://github.com/gear-genomics/tracyThank 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