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Old 06-07-2010, 07:07 AM   #50
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Originally Posted by Thomas Doktor View Post
The qualities look fine so it's not an issue of bad base calling. I think you could be right that the cluster calling and/or sequencing chemistry could explain some of it. Could perhaps explain why certain sequences in the genome are less likely to be sequenced, we often see peaks and valleys in exons in our RNA-seq runs which are most likely explained by sequencing artefacts.
I have seen the same phenomena but only with our mRNA-Seq libraries. Our genomic libraries do not show any biases. Has anyone else experienced this? Could it be an artifact of the Illumina library preparation protocol, may be at the fragmentation step?
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