Hi,
we adapted HLA typing (amplicons of exons 2+3 with own primers) from Roche 454 to MiSeq. Now I have the problem that certain DRB1 alleles show many errors in the forward read 1 for exon 2, although I have perfect coverage of reverse read 2. And other similar alleles amplified with the same primers do not show those errors and have good coverage.
Has anyone seen similar problems, that a certain sequence somehow can't be sequenced?
Could it be that PhiX interfers?
I don't now what else I can do?
Thanks for helping,
Barbara
we adapted HLA typing (amplicons of exons 2+3 with own primers) from Roche 454 to MiSeq. Now I have the problem that certain DRB1 alleles show many errors in the forward read 1 for exon 2, although I have perfect coverage of reverse read 2. And other similar alleles amplified with the same primers do not show those errors and have good coverage.
Has anyone seen similar problems, that a certain sequence somehow can't be sequenced?
Could it be that PhiX interfers?
I don't now what else I can do?
Thanks for helping,
Barbara
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