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Old 08-28-2017, 11:45 AM   #4
Brian Bushnell
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Location: Walnut Creek, CA

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With TruSeq the shearing and adapters are independent, so I suppose it depends on your shearing process. I don't have any data for this but I would expect any enzymatic process to incur bias but sonication much less so. You can always test whether the uneven base composition is genomic or synthetic by mapping and calculating the mismatch rate by read position. If it is no higher at the spiky 3' end then the spikes are genomic and just caused by bias. If there is a high mismatch rate they are probably synthetic and should be trimmed, but I have never seen that happen in a normal fragment library.
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