Claudia Calabrese

Hi, This is expected, especially with very high read depth. Did you run the analysis on human samples? And what was the average per sample read depth? In our hands,...

Hi, a difference between RCRS and RSRS-based variant calling is indeed expected. The reason is that RSRS is better suited for haplogroup prediction, being a virtual reference sequence based at...

Also, I would suggest couple of useful readings about rCRS and RSRS differences, most importantly the Behar et al paper from 2012: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3322232/

Can you please copy-paste the HG00119.conf file you're using? It looks like an error due to the working directory where your input files are placed /home/juan/Desktop/MToolBox-master/MToolBox/test/HG00119_example/ does not exist.

Hi, apologies for the late reply. 1. the current version of MToolBox is not meant to be used for RNA-seq. However, given the lack of splicing in mtDNA genes, the...

Hi, Is this issue still open? If so, did you export the full path to MToolBox, by doing: export PATH="/path/to/MToolBox/:$PATH" before running the `MToolBox.sh` script? best C

Hi, we didn't test MToolBox on IonProton sequences yet, but it would be good to check if it is compatible with that technology. What is the average length of the...