Hi, I've been having an unusual problem with my reads. I've been doing exome sequencing on a HiSeq 2000, but I'm getting only about 40% GC content at the start of each read, climbing to 45-50% closer to the centre. At first I thought this was due to PCR bias. Changing my PCR protocols helped a bit, but there's still a very strong positional effect which I don't think can be explained by PCR alone. Has anyone seen something like this before?
We're using a Bioruptor for shearing as we don't have access to a Covaris. Is it possible that the Bioruptor is preferentially shearing in AT-rich regions? Is there any way to avoid this?
We're using a Bioruptor for shearing as we don't have access to a Covaris. Is it possible that the Bioruptor is preferentially shearing in AT-rich regions? Is there any way to avoid this?
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