Hello,
I have been sequencing NimbleGen Array-captured samples on the SOLiD and seeing strikingly low matching percentages (20-40%). This has occured on human exome captures and mouse captures. Before matching I run a script that finds the NimbleGen adaptor and trims it off the read leaving me with a set of 30bp reads and an untrimmed set of 50bp reads. Both of these sets match poorly, though the 50bp reads are worse. Does anyone have any experience with sequencing captured DNA on the SOLiD? Thanks.
I have been sequencing NimbleGen Array-captured samples on the SOLiD and seeing strikingly low matching percentages (20-40%). This has occured on human exome captures and mouse captures. Before matching I run a script that finds the NimbleGen adaptor and trims it off the read leaving me with a set of 30bp reads and an untrimmed set of 50bp reads. Both of these sets match poorly, though the 50bp reads are worse. Does anyone have any experience with sequencing captured DNA on the SOLiD? Thanks.
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