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Old 10-27-2015, 11:48 AM   #1
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Location: Louisiana

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Default Amplicon poor alignment on one sample

We ran 20 FFPE samples on Illumina miSeq using the Swift 56g oncology panel. We trimmed the primers off and then aligned to the human genome.
19 samples aligned well (89-94%) while one sample aligned only at 68%. Since I do not have much experience with the amplicons, I am looking for help.

My collaborator says we should proceed by using all the data, including the aligned reads from this "bad" sample. I suggested to remove this "bad" sample as we should not use these reads even if they are aligned, before we proceed the steps of the workflow to find the variants.

What would you do in this scenario?

Thank you,

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