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This issue has been mentioned before, but with Debian stretch it has changed. I have a 15inch touchscreen that will not calibrate with the usual x-input that debain jesse had. I have tried to run the calibrator, it plots the 4 points and i save the ouput in the ****99 file as usual, the problem is the axis are inverted. I have set the inverted flag to 0 and 1, but no difference. Does someone have an up to date guide?

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I found the procedure in https://gist.github.com/KurtJacobson/37288a0300a9c1b3e859c8dcff403300 to be very helpful in getting a touchscreen calibrated under Raspbian stretch. Since Raspbian is based on Debian, the procedure applies. But before you start, edit your 99-calibration.conf file to delete or disable its transformation matrix.

Once you've fined-tuned your transformation matrix, you'll need to save it in ~/.xsessionrc so it will apply every time the system reboots. Here's mine as an example.

#!/bin/bash

# Set coordinate transformation matrix for Pi-RAQ touch display
# (rotate left; adjust for accurate pointer tracking)
xinput set-prop 'TSC-50 DMC' 'Coordinate Transformation Matrix' 0 1.05 -0.025 -1.6 0 1.3 0 0 1
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Vote up for Mark Bersalona's answer!

I just needed to rotate the touchscreen 180 degrees, no calibration. I followed the steps in the link https://gist.github.com/KurtJacobson/37288a0300a9c1b3e859c8dcff403300. Note that the interactive tool can't rotate 180. Found more information about this on https://wiki.ubuntu.com/X/InputCoordinateTransformation. Also note that you need to run the commands on the screen on the actual unit, not from SSH.

This command solved my problem:

xinput set-prop 'FT5406 memory based driver' 'Coordinate Transformation Matrix' -1 0 1 0 -1 1 0 0 1

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