I don't know if anyone has asked about this in the forum before. I have difficulty understanding what "gap-fill" is and when/how does the program gap-fill. I am currently using version 4.18.
For instance, under the EIC plot window on the top, there is a table-viewer function on the right-click menu where I can view chromatograms of the specific alignment across samples. In one of the columns, it tells whether the peak was gap-filled (shown as -2) or not. However, what I don't understand is the last column where it shows the peak with points in the chromatogram: for those that are gap-filled, does it make up the points of a peak? If it is gap-filled meaning that the peak does not exist, why would it create points of a non-existing peak? On the other hand, if the points were based on an actual/existing peak, why would the program gap-fill? If it sounds confusing and you prefer some screenshots, please let me know. I appreciate your help!