Hi All,
We did an exome capture using the IDT exome panel, 12 samples per capture. To increase the data throughput per sample, the same capture pool is sequenced in two PE100 HiSeq lanes.
When the data of only one lane is analyzed, the raw coverage is 96X, while usable reads (mapped to exome and removed duplicates) covered 55X (duplication rate = 20%). Yet when data of both lanes are analyzed together, raw coverage is roughly doubled (192X), but the usable reads became 88X (less than double of 55X), and duplication rate raised to 40%.
Does any of you have experience in using IDT exome panel for capture? What are the percentage of usable reads, and duplication rate, respectively?
Are there better ways to increase data throughput, while retaining high usable reads coverage?
Million thanks!
Hin
We did an exome capture using the IDT exome panel, 12 samples per capture. To increase the data throughput per sample, the same capture pool is sequenced in two PE100 HiSeq lanes.
When the data of only one lane is analyzed, the raw coverage is 96X, while usable reads (mapped to exome and removed duplicates) covered 55X (duplication rate = 20%). Yet when data of both lanes are analyzed together, raw coverage is roughly doubled (192X), but the usable reads became 88X (less than double of 55X), and duplication rate raised to 40%.
Does any of you have experience in using IDT exome panel for capture? What are the percentage of usable reads, and duplication rate, respectively?
Are there better ways to increase data throughput, while retaining high usable reads coverage?
Million thanks!
Hin
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