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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
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