Question: percent methylation in CHH file of Bismark?
1
gravatar for ahsan.raza.rana
3.0 years ago by
ahsan.raza.rana40 wrote:

Hi, I have generated a file by cytosine report function in bismark to calculate even the non CpG methylated Cs(CHH,CHG). The file of CHH shown as follow:

 > chr1 3000001 -   0   0   CHH CNN
    chr1    3000006 +   0   0   CHH CTT
    chr1    3000011 +   0   0   CHH CTA
    chr1    3000015 -   0   0   CHH CAT
    chr1    3000021 -   0   0   CHH CTA
    chr1    3000030 -   0   0   CHH CAT
    chr1    3000038 -   0   0   CHH CCA
    chr1    3000039 -   0   0   CHH CCC
    chr1    3000041 -   0   0   CHH CAC
    chr1    3000054 +   0   0   CHH CTT
    chr1    3000059 -   0   0   CHH CAA
    chr1    3000061 +   0   0   CHH CCT
    chr1    3000062 +   0   0   CHH CTT
    chr1    3000065 +   0   0   CHH CTT
    chr1    3000073 +   0   0   CHH CCT
    chr1    3000074 +   0   0   CHH CTA
    chr1    3000082 +   0   0   CHH CTT
    chr1    3000086 -   0   0   CHH CTA
    chr1    3000087 -   0   0   CHH CCT
    chr1    3000091 -   0   0   CHH CAA
    chr1    3000092 -   0   0   CHH CCA

I have to calculate the total coverage at each location and % methylation and for this the formula i know is

`column4 of '+' strand + column5 of '+' strand + column4 of '-' strand + column5 of '-' strand]= total coverage`

and percentage was equal to [($4/$4+$5)*100 of '+'strand +($4/$4+$5)*100 of -strand]/2 but this could only b possible in CpG cytosine covergae and CHG coverage files that have output format like:`

chr1    3000035 +   0   0   CHG CTG
chr1    3000037 -   0   0   CHG CAG
chr1    3000045 +   0   0   CHG CAG
chr1    3000047 -   0   0   CHG CTG`

means alternate + and negative strand. But in CHH file there are no alternate strands and even the gaps between the values is not consistent. I dont know how to calculate these values. Should I do it for each single line means total coverage will be then sum of column 4 and 5 and not to bother about + strand or its relative negative strand.Any suggestions

next-gen • 1.4k views
ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by ahsan.raza.rana40
3
gravatar for Devon Ryan
3.0 years ago by
Devon Ryan89k
Freiburg, Germany
Devon Ryan89k wrote:

For CHH sites you calculate each line, there is no merging of lines because there are no C's on the opposite strand to merge with.

ADD COMMENTlink written 3.0 years ago by Devon Ryan89k
0
gravatar for ahsan.raza.rana
3.0 years ago by
ahsan.raza.rana40 wrote:

thanks alot. I am really grateful

ADD COMMENTlink written 3.0 years ago by ahsan.raza.rana40
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