Methyldackel not providing full output

Hi all,

I’m encountering an issue when using methyldackel to extract methylation information.

According to the documentation, the output of methyldackel should be six columns, including:

  1. The chromosome/contig/scaffold name
  2. The start coordinate
  3. The end coordinate
  4. The methylation percentage rounded to an integer
  5. The number of alignments/pairs reporting methylated bases
  6. The number of alignments/pairs reporting unmethylated bases

However, when I run methyldackel, I only get four columns. This includes columns 1-3 from above (chromosome ID and coordinates), plus one additional column that is an integer (sometimes >100, but generally ~1-10); not sure if this corresponds to columns 5 or 6 from above.

I haven’t been able to figure out why I’m not getting all six columns, and I’m wary about running differential methylation analysis on the data I’m receiving.

Any help would be greatly appreciated; thank you!

Hi @Shanna

This tool has an option near the bottom of the form named Output options.

The default methylation output is what you are describing but the others differ.

Which output option did you choose?

If you want to share the tool settings (screenshot or copy/paste from the “i” page), or your entire history, both would provide context for the job and we’ll be able to help more specifically. How to → How to get faster help with your question

Thanks! :slight_smile:

Hi @jennaj

I see - it seems like this may be the issue! I’m using a workflow, and the “output options” are set to CpG methylation counts (see screenshot).

I assume the first option (CpG context methylation metrics) is the default?

Thank you so much!

Screenshot 2024-06-10 at 6.06.13 PM

Hi @Shanna

This is the default:

Screen Shot 2024-06-11 at 9.41.49 AM

You should be able to adjust that in your workflow – just watch out for any downstream tools that are reading the result file in – since those would be expecting the original output format.

Hi @jennaj ,

Sounds good, thank you so much for your help!

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