‘Because when we use low pass there will be a little phase shift and it can effect the transfer function of the system.’
You are correct to recognise that possibility, however it is straightforward to avoid using the filtfilt function to do the actual filtering of the signal with any filter you design. The lowpass function does this automatically. For best results with it (and its friends) use the ImpulseResponse','iir' name-value paiir.
For broadband (not band-limited) noise use the sgolayfilt funciton. I usually use a 3-degree polynomial and adjust the ‘framelen’ value to get the result I want.
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