QDD VM does not boot

You followed the installation process described here but at point 6 the VM does not boot.

Try to disable the USB2 controller

1. Open VirtualBox Manager
2. Select VM
3. Select Settings, then USB
4. Uncheck Enable USB 2.0 (EHCI Controller)
5. Start VM

Primer3 error message: 'Unable to open file primer3_config.stack.ds'

QDD is running but you have error messages from primer3 and no primer is designed

1. Make sure you have set correctely the path to primer3_core(.exe) in the set_qdd_default.ini file
2. If it does not help, move the primer3_config folder to the directory where primer3_core is found

PCR product size - primer position

PCR product size does not match with primer positions in the sequence

The primer positions are given as it was in the output of primer3. However, in some cases, one or even both primers can match more than once the underlying sequence. In these cases, the sequence of the PCR product (PCR_PRODUCT_SEQ) and the length of the PCR product (PCR_PRODUCT_SIZE) are given for the longest PCR product. On the other hand, the primer – target region distance (MIN_PRIMER_TARGET_DIST) is given for the shortest PCR product. This decision was based on our lab results were we found that longer PCR products and primer pairs close to the target regions are less likely to give a clear genotyping profile (Meglecz et al. 2014).

If primers match more than once the sequence, the PCR_PRIMER_ALIGNSCORE is high, and these primer pairs are very unlikely to be flagged as the "best pair" for the sequence (ONE_PRIMER_FOR_EACH_SEQ).

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