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Is this mostly a theoretical question?
Sometimes we encounter exceptional libraries that will sequences well even with read numbers above spec (rare). In general, over-clustering will lead to drop in Q scores. The drop may be spread across the run or may be more towards the ends of reads (if the run was borderline over-clustered).
Whether Q score trimming can help will depend on the data you have.
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The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...-
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07-08-2024, 03:19 PM -
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