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nextgenusfs avatar nextgenusfs commented on August 20, 2024

For ion preprocessing the forward primer is required, along with a valid barcode sequence. The reverse primer is removed if it is found. https://amptk.readthedocs.io/en/latest/pre-processing.html

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bsmoda avatar bsmoda commented on August 20, 2024

If not found, the read is maintained or is dropped from the processing?

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nextgenusfs avatar nextgenusfs commented on August 20, 2024

Reads without valid barcodes or forward primers are discarded in the ion workflow. Not sure what isn’t clear in the docs?

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bsmoda avatar bsmoda commented on August 20, 2024

I think is clear now. I didn't understand that only forward primer is necessary for the processing. I thought that only the read would pass the processing if both primers forward and reverse were present in the read.
That helps a lot, thank you Jon!

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