hydroxymethylation

[Elitsa Stoyanova]

Hello,

 

I was wondering if it is possible to run MLML to get the hydroxymethylation levels and then somehow create a .meth file that can be used for roimethstat. Or alternatively, is there another way to calculate hydroxymethylation over a certain interval using methpipe? Thanks!

Best,

Eli

[Jianghan Qu]

Hi Eli, 

With roimethstat, you might need to carefully create pseudo read coverage numbers. However, for your purpose, bedtools (http://bedtools.readthedocs.io/en/latest/)  might be a better choice. 

Suppose the output from MLML is a file mlml.out

You can create a bed file with the 5th column containing the hydroxymethylation levels by the following awk command

awk 'BEGIN{OFS="\t"} {print $1,$2,$3, "hmC", $5, "+"}' < mlml.out > mlml_hmC.bed

Now use bedtools map command: 

bedtools map -a interval.bed  -b mlml_hmC.bed -o mean > interval_hmC_levels.txt

The interval-average hydroxymethylation levels are in the last column of  interval_hmC_levels.txt

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Jenny

[Chris S]

Hi Jianghan,

I think this is related to the original question. The MLML output appears to not be compatible with tools in the manual such as radmeth, because the output is very different. If I have 8 files of MLML output (4 control, 4 treatment), how could I approach the changes in hydroxymethylation and have support of statistics?

Thanks,

Chris

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Jenny