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I'm trying to combine multiple clips and remove the silence between them but there is an obvious short pause that leads to a "skipping" quality to the overall track when combined. I've tried removing the silence on the combined file but it's still leaving traces of dead silence that leave that skipping sound. Is there an easier way to remove these silent portions by automatically placing the clips over each other using a manual overlap measurement, or is there another way to scan for silence that lasts less than 10ms?
There is no automatic way of doing this other than the one you are already using... One thing to note though is that the position of the 'signal is below/above' settings can make a big difference to how much silence is left. The lower the threshold values, the bigger the remaining gaps get, as the audio will have to fall further towards silence before anything happens - if you see what I mean. Also, I think it's more reliable to use Shorten Silence - and have it set to 0ms.
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There is no automatic way of doing this other than the one you are already using... One thing to note though is that the position of the 'signal is below/above' settings can make a big difference to how much silence is left. The lower the threshold values, the bigger the remaining gaps get, as the audio will have to fall further towards silence before anything happens - if you see what I mean. Also, I think it's more reliable to use Shorten Silence - and have it set to 0ms.
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It has also occurred to me that the other thing that will affect the performance of this is the settings you have in Edit>preferences>Data. By default these are set so that delete/cut boundaries are smoothed by 2mS and all edit boundaries have a 5ms crossfade applied to them. If you reduce these settings, then clicks are rather more likely to occur, because no proper account will be taken of zero-crossing errors - which always produce clicks.
As far as placing them in multitrack using an overlap - well you can do that, certainly, but there's no automatic placement facility. Neither should there be - this is always something best done by ear, remembering that people only assimilate what they've heard in the gaps in speech. The more complicated a sentence, generally the longer the gap should be...