Hi All,
This is my first post, although, I have been reading all your posts for a while. So thanks!
We have been playing with some whole exome capture experiments here in Exeter using SureSelect. We get good on target figures, on par with those in the literature.
We have come across some issues that I’m sure you are all aware of, but I wasn’t so I thought I’d post. Hope it is of interest.
Whole exome only really means around 75% of the RefSeq genes in build HG18. Nimblegen say 75%, we couldn’t get a figure from Agilent but a quick and dirty gene name count came out with 82%.
Also start and end co-ordinates in the .bed file for Agilent do not always cover the whole coding region of an exon. They do mostly, but I have found examples of when using the .bed file to return the targeted sequence, only half an exon is covered.
This is my first post, although, I have been reading all your posts for a while. So thanks!
We have been playing with some whole exome capture experiments here in Exeter using SureSelect. We get good on target figures, on par with those in the literature.
We have come across some issues that I’m sure you are all aware of, but I wasn’t so I thought I’d post. Hope it is of interest.
Whole exome only really means around 75% of the RefSeq genes in build HG18. Nimblegen say 75%, we couldn’t get a figure from Agilent but a quick and dirty gene name count came out with 82%.
Also start and end co-ordinates in the .bed file for Agilent do not always cover the whole coding region of an exon. They do mostly, but I have found examples of when using the .bed file to return the targeted sequence, only half an exon is covered.
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