Jordi Abante

Hi Lucas, I will try to debug this with you. It looks like the previous step only generated files for the first chromosome. Can you tell me what command did...

Okay, so I understand that you submitted a single job for the `for` loop you shared with me? We recommend submitting an individual job per each chromosome for each sample....

I see, so that confirms that something went wrong in a previous step for the rest of the chromosomes. That is why both `singleMethAnalysisToBed.sh` and `diffMethAnalysisToBed.sh` are only generating output...

I see, alright. So the size of the `.mat` files for the reference look just fine. However, the size of the `_matrices.mat` files seems to be a bit smaller than...

Sounds good. So the sizes we usually see for human data are between 15-30G's. That usually translates into average coverages of x20. In our experience, WGBS data that is ~125bp...

I see yes, it looks like some sort of targeted BS. We are not familiarized with this type of data, but as long as the reads are distributed uniformly within...

Thank you so much for your feedback, this was very helpful.