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Old 12-19-2018, 08:26 AM   #1
cascoamarillo
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Location: MA

Join Date: Oct 2010
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Default In-silico control

Hi,

Just a quick one: how can I generate an in-silico control for modification analysis with my genome and my PacBio reads? So it predicts the IPD using the local sequence context around the current position. I have seen this in:

https://github.com/fanglab/SMRTER

Where it compares IPD ratios with a control, either a natural control (with wga reads) or an in-silico type.

On the same thread, reading Beaulaurier et al. 2015 (BioRxiv) it is mentioned the creation of a negative control, instead of a wga, by randomly shuffling IPD values among molecules. Are we taking about the same type of control (in-silico=shuffling IPD)?

Thanks
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