Hello everyone,
I am in the process of designing custom SureSelect baits for several different genomic regions. I have a list of SNPs that we would like to have sequenced. The problem is that some of the SNPs are within repetitive elements. The default setting for the Agilent's eArrary software are set for a maximum bait overlap of 20bp with repetitive sequence. I have found that increasing the allowed overlap to 50bp gives bait coverage to several of the SNPs that are not covered with the default 20bp overlap.
I wanted to know if anyone has increased the bait/repetitive element overlap to 50bp. I can image that this could result in the pull-down and sequencing of many unwanted repetitive elements resulting in wasted sequence. Any thoughts would be great.
Thanks,
DoubleA
I am in the process of designing custom SureSelect baits for several different genomic regions. I have a list of SNPs that we would like to have sequenced. The problem is that some of the SNPs are within repetitive elements. The default setting for the Agilent's eArrary software are set for a maximum bait overlap of 20bp with repetitive sequence. I have found that increasing the allowed overlap to 50bp gives bait coverage to several of the SNPs that are not covered with the default 20bp overlap.
I wanted to know if anyone has increased the bait/repetitive element overlap to 50bp. I can image that this could result in the pull-down and sequencing of many unwanted repetitive elements resulting in wasted sequence. Any thoughts would be great.
Thanks,
DoubleA