Comments (4)
I had the same issue. Just download the methratio.py script from GitHub and replace it with the one you used previously. The issue arises because of the samtools -X option in the old script. Hope that helps!
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You're welcome @NaKent. You should check your methratio.py output files to see if they have any data at all. If they do, then, it should work. I recommend following the methylkit tutorial: https://bioconductor.org/packages/devel/bioc/vignettes/methylKit/inst/doc/methylKit.html
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Thank you very much!! The problem was solved.
If you don't mind, I want to ask unrelated question. (Sorry, I'm stranger to this field.)
I tried to run DMR with MethylKit, but the format of methylation ratio file on this BSMAPz seems to be different from original BSMAP's one.
So, THIS PAGE is no longer helpful for me. How can I do DMR with the result of methratio.py?
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Thank you for your help.
After I learned the page and awk, I achieved analyzing the data with R :)
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Related Issues (20)
- Segmentation Fault when Loading Reference HOT 3
- methratio exception HOT 8
- query regarding methylation level from methylratio output file. HOT 1
- Float point error in methratio.py HOT 4
- methratio.py error
- ZeroDivisionError: float division by zero HOT 1
- Significantly different in number of covered cytosines between bsmap 2.90 and BSMAPz HOT 4
- Segmentation fault - core dumped
- methratio.py and Identification of methylated cytosine sites
- OverflowError in methratio.py
- methdiff.py error HOT 1
- "Illegal instruction" message when I launch bsmapz
- When I run the script I get the error CMD: R --vanilla HOT 1
- methratio.py AssertionError HOT 3
- Methratio.py does not handle files HOT 4
- "AssertionError: String length does not match CIGAR" when running methratio.py
- methratio.py memory issue
- How to calculate sequencing depth HOT 1
- methratio.py ERROR in conda and multicores of CPU: list index out of range
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