Comments (4)
@ryansohny I appreciate that you brought this up. Today we added a check for this in each place where that file format is loaded (6 different commands I think). The error messages aren't great yet, but at least users will be informed of a problem if those values are not in the expected range.
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@ryansohny The counts format we use has methylation as fractional. I think you somehow made it into percentages.
https://dnmtools.readthedocs.io/en/latest/counts/
If this turns out to be the only source of your problem, I'll relabel this issue as a need for input validation.
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Wow this is embarassing. A classic example of "why you should read the manual carefully".
When I created an input from the same sample sequenced in a different way (WGBS), I formatted it in the right way (fractional) so I guess I must have been distracted for some reason.
And I got what I want! It went smoothly.
Thank you very much Professor Smith. Wish you all the best.
Sohn
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That's great news! Always grateful for developers who go the extra mile to make things easier for their users. Much appreciated it!
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Related Issues (20)
- selectsites failing with poor message on unsorted sites processed on disk
- dnmtools diff Error HOT 4
- Calling HMRs on the DNA Methylation Atlas Data HOT 4
- roi "cannot sort data unless all data is loaded" HOT 3
- mlml "error: chrom or pos mismatch in both files" HOT 3
- Keep non-CpG sites after sym command
- Broken progress bar
- roi -M return different values for "number of CpGs in the region" for different count files HOT 3
- roi should check for input files before reporting any problems with arguments
- pmd crash if insufficient data unless verbose mode used HOT 1
- -v flag opposite in guessprotocol
- A question for 'dnmtools allelic' HOT 2
- format: max distance when merging mates seems ignored
- merge -t header seems to be not properly formatted HOT 3
- HMR crash when nothing identified
- bad count line HOT 1
- resolved.
- unknown vectorizer cost model ‘very-cheap’ HOT 6
- summary hmr_count is non-zero but hmr output file is empty HOT 5
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