Hello!
I'm new to PacBio and NGS sequence analysis, so I hope someone here can point me in the right direction.
I have 1 SMRT cell worth of sequencing data (just a pilot for now).
The sample is a mix of libraries (amplicons) of about 800 bp. Each of these libraries is derived from one and the same gene, but they've been through a mutagenic process and should carry some diversity = 1-10 SNPs per molecule, relative to the reference.
We have a non-mutagenized wild-type library in the sample as well.
All of these libraries are barcoded. The amplicon structure is:
Barcode - Amplicon - Universal_primer.
Even though barcoding was not exactly done according to PacBio barcoding recommendations, I feel resolving barcodes will not be a huge problem. However, calling variants might be difficult. Does anyone here have experience with reliably detecting SNPs in samples with similar characteristics?
I'm new to PacBio and NGS sequence analysis, so I hope someone here can point me in the right direction.
I have 1 SMRT cell worth of sequencing data (just a pilot for now).
The sample is a mix of libraries (amplicons) of about 800 bp. Each of these libraries is derived from one and the same gene, but they've been through a mutagenic process and should carry some diversity = 1-10 SNPs per molecule, relative to the reference.
We have a non-mutagenized wild-type library in the sample as well.
All of these libraries are barcoded. The amplicon structure is:
Barcode - Amplicon - Universal_primer.
Even though barcoding was not exactly done according to PacBio barcoding recommendations, I feel resolving barcodes will not be a huge problem. However, calling variants might be difficult. Does anyone here have experience with reliably detecting SNPs in samples with similar characteristics?
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