You can do dark frame subtraction, this is the preferred way to eliminate hot pixels; you will also reduce the fixed pattern noise in the process. Hot pixels are just an extreme case of fixed pattern noise. Dark frame subtraction is the best technique for supressing hot pixels, because it uses direct knowledge of the position, color and relative brightness of these pixels, rather than post-hoc (noise reduction) techniques, which must guess at what is noise and waht is signal.
Make sure that your dark frame is taken under the same conditions, preferrably immediately after the exposure to which it is to be applied. Take it using the same camera settings, including the exposure time, ISO, and any in-camera settings such as white balance, sharpening, etc.
The frame can be subtracted from the exposure in almost any image editor that supports layers.
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