quickstart - calling methylation with nanopolish issues

[daanverhagen]

hi, a couple of things i noticed when running through the tutorial mentioned in the title:

The compare_methylation.py is slightly broken. I followed the quickstart guide and when i got to the plotting it threw an error. The issue was due to a difference in column names. it looks for a column names "num_cpgs_in_group" but cant find this because the column is referred to as "num_motifs_in_group". simply changing the column name in either the .tsv or .py fixes this.

I should also note that the calculate_methylation_frequency.py script was missing from example dataset but i found it in the scripts list

I also wanted to note that the steps for aligning to the reference genome does not appear to be working as intended. I circumvented this issue by manually performing the following 4 steps

• minimap2 to make sam file
• samtools view to convert sam to bam,
• samtools sort to sort
• samtools index to index from here on out the quickstart guide works as described aside from before mentioned small issues

sorry for the multiple comments in a single issue. perhaps these issues were due to me using a new/old version. If so i'd like to best regards

[jts]

Thanks for letting us know the problems you had. @jopineda is currently revising the tutorial - Joanna can you make sure these comments are addressed?