bismak_methylation_extractor files into methylkit

[KARAN PATEL]

Hi

i am new methylkit. i want to perform differential methylation. i want to know that how do i take the bismak_methylation_extractor files into methylkit.

chrBase	chr	base	strand	coverage	freqC	freqT
chr21.9764539	chr21	9764539	R	12	25.00	75.00
chr21.9764513	chr21	9764513	R	12	0.00	100.00
chr21.9820622	chr21	9820622	F	13	0.00	100.00
chr21.9837545	chr21	9837545	F	11	0.00	100.00
chr21.9849022	chr21	9849022	F	124	72.58	27.42
chr21.9853326	chr21	9853326	F	17	70.59	29.41

I want this type of file.

[Abdul Rawoof]

Hello Karan,

You can use readBismarkCytosineReport function to import bismark generated report which is generally have following information

#Chr                #pos         #strand      #mCs         #Ts             #context     #bases

Chr01        67      +       0       1       CG      CGA
Chr01        68      -       0       0       CHH     CGT
Chr01        192     +       1       0       CHG     CGT
Chr01        193     -       2       7       CG      CGA
Chr01        239     +       0       1       CHG     CGA
Chr01        240     -       1       7       CG      CGT
Chr01        339     +       0       0       CHH     CGA

Hope you get the answer.

Best,

Abdul Rawoof