MTR

[YibingZeng]

Hi Dr. Guo,

When I tried to do the MTR analysis, I find out result as followed: 1 21800 21991 NA 0 NA 0

But when I trace back to the CGmap.gz file, I can clearly see that there is methyaltion there: 1 C 21823 CG CG 1.0 1 1 1 G 21824 CG CG 1.0 2 2 1 C 21845 CG CG 1.0 1 1 1 G 21846 CG CG 1.0 2 2 1 C 21849 CG CG 1.0 2 2 1 G 21850 CG CG 0.5 1 2 1 C 21851 CG CG 1.0 2 2 1 G 21852 CG CG 1.0 2 2 1 C 21853 CG CG 1.0 2 2 1 G 21854 CG CG 0.0 0 2 1 C 21882 CG CG 1.0 1 1 1 G 21883 CG CG 1.0 1 1 1 C 21897 CG CG 1.0 2 2 1 C 21912 CG CG 1.0 2 2 1 C 21914 CG CG 1.0 2 2 1 C 21926 CG CG 1.0 2 2 1 C 21939 CG CG 1.0 2 2 1 C 21953 CG CG 1.0 2 2 1 C 21975 CG CG 1.0 4 4

The command I used for the analysis is: cgmaptools mtr -i rep3CHG.gz -r ${MITE} -o B73_rep3_CHG_MITE.mtr

Would you please tell me how can I fix this problem?

Yibing

[guoweilong]

Hi Yibing,

Are you working on correct files? Your file name is "CHG", but all the sites you pasted here are in CG context.

Best, Weilong Guo

[YibingZeng]

Sorry for that, the command I use is: cgmaptools mtr -i rep1CG.gz -r ${MITE} -o B73_rep1_CG_MITE.mtr

[YibingZeng]

19 Provide two methods to fix the problem, one is to change python3 to python2, another one is to sort the file. I think I will try them. If you have better solution, please let me know as well.

Hope you do well. Yibing

[guoweilong]

Yes, python version and sorting seems be required. Wish to read your feedback.

[YibingZeng]

It works. But if the regions are overlapping, only the first region would be calculated. The problem of there is coverage but could not be called was solved!

[guoweilong]

Em, yes. Current version is for sorted non-overlapping regions. Maybe we'll figure out how to applied it to regions with overlap.