Hi
I did whole-genome sequencing and whole-exome sequencing on a whole-genome amplified (WGA’d) sample and got 2% of reads removed as duplicates by whole-genome sequencing but 80% of reads removed by whole-exome sequencing.
I then did whole-exome sequencing on an unamplified HapMap control and WGA’d HapMap control and got 25% of reads removed from the unamplified HapMap control and 50% removed from the WGA’d HapMap control.
I used Illumina standard PE101 whole-genome sequencing protocol for whole-genome sequencing and NimbleGen exome capture (version 2) for exome capture followed by Illumina sequencing.
Can anyone share some thoughts on the big difference between whole-genome sequencing and whole-exome sequencing of my WGA’d sample in terms of duplicate removal? All your comments will be greatly appreciated!
I did whole-genome sequencing and whole-exome sequencing on a whole-genome amplified (WGA’d) sample and got 2% of reads removed as duplicates by whole-genome sequencing but 80% of reads removed by whole-exome sequencing.
I then did whole-exome sequencing on an unamplified HapMap control and WGA’d HapMap control and got 25% of reads removed from the unamplified HapMap control and 50% removed from the WGA’d HapMap control.
I used Illumina standard PE101 whole-genome sequencing protocol for whole-genome sequencing and NimbleGen exome capture (version 2) for exome capture followed by Illumina sequencing.
Can anyone share some thoughts on the big difference between whole-genome sequencing and whole-exome sequencing of my WGA’d sample in terms of duplicate removal? All your comments will be greatly appreciated!
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