NAs of methylpy add-methylation-level result

[liyangyang12]

Dear yupenghe,
When calculating the methylation level of genome regions with "methylpy add-methylation-level", there are a lot of NAs, but there are methylation sites on IGV, why?
methylpy add-methylation-level results

IGV

Thanks.

[yupenghe]

Hey liyangyang12,
Do you mind to provide more details about this issue? Specifically,

• what is the full command you used to run methylpy add-methylation-level?
• do all regions in this contig/chromosome have NA values in all samples?
• could you share one allc file (and the corresponding idx file) for one sample that has data in this region?

[liyangyang12]

Hey yupenghe,
I read your previous answer and found that I did not sort the bed file, now the problem is solved.
Thanks a lot for your time and effort!

[liyangyang12]

Hey yupenghe,
By the way, what is the difference between 0 and NA in the result of methylpy add-methylation-level?
Can I replace NA with 0?

[yupenghe]

Cool. Glad that it is solved. NA means no coverage (and in this case, methylp was able to find the correct CpG data for some regions due to BED file being unsorted). 0 means 0/N fragments that support methylation where N is the number of fragments covering the CpGs in the region and N>0.

[liyangyang12]

ok. thank you！