Table 3.

Troubleshooting table.

Steps	Problem	Possible reason	Solution
Step 1	In Fiji ImageJ the gel image shows in negative colors.	Lookup table is set incorrectly.	Click Image->Lookup Tables-> Invert LUT
Step 9	The semi-automatic algorithm cannot identify all needed band locations on HRF profile.	The data is too noisy or the magnitude of the peaks is very small.	1) Try to adjust parameters so that only well resolved peaks are clearly identified. Click on the Interpolate switch to guess the missing positions.  2) If the previous option does not solve the problem: write down the positions of bands that are still missing by placing the mouse pointer at these locations. Refer to instruction in lane_config.csv file on how to specify these locations manually in the addpeaks column.
Step 20	On the resulting plot the individual Gaussians describing bands at the end of the gel are too broad to represent a physically plausible solution.	Overfitting has occurred.	Use a more stringent fitting constraint option, for example, “SIGMA=k*D+b”
Step 27	Theoretical DNA cleavage profiles look noisy	Small irregularities in 3D structure can affect deoxyribose hydrogen atom accessibility.	Use only contributions from H4’, H5’ and H5’’ deoxyribose hydrogen atoms to estimate cleavage profile. Set Hcontrib parameter to [0,0,0,0,1,1,1]