Can BSMAP calculate the coverage/ percentage of all CpGs covered in the reference?

[illuminaGA]

Hi everyone.

I have a basic question. My bisulfite sequencing data was mapped by BSMAP, but I am not sure how to calculate the coverage/ percentage of all CpGs covered in the reference genome.

I check the README file but didn't find some hint.

Any help would be appreciated!

[dpryan]

No, it can't. If you used PileOMeth to extract the CpG metrics in bedGraph format, then you could use bison_CpG_coverage from Bison to get what you want. It might also be the case that bismark includes a tool for this, I don't know.

[illuminaGA]

Thank you so much!

Nice to talk with you. I noticed that you are the author of Bison.

May I know how did you calculate the percentage of CpG coverage?

No, it can't. If you used PileOMeth to extract the CpG metrics in bedGraph format, then you could use bison_CpG_coverage from Bison to get what you want. It might also be the case that bismark includes a tool for this, I don't know.

[dpryan]

What bison_CpG_coverage does is:

1. Read in the genome
2. Iterate through the genome, finding each CpG
3. Iterate through a sorted bedGraph file, line by line
4. If a genomic CpG is in the bedGraph file, it increments a bin denoting its coverage (e.g., if a site has 10x coverage then the 10x counter is incremented)
5. If a site isn't in the bedGraph file, the 0x counter is incremented
6. At the end, the counters are output into a text file

The resulting file is convenient for analysis in R or even with awk. You can easily compute percentage of bases with >=1x or >=10x coverage with simple arithmetic.

[alim123]

No, it can't. If you used PileOMeth to extract the CpG metrics in bedGraph format, then you could use bison_CpG_coverage from Bison to get what you want. It might also be the case that bismark includes a tool for this, I don't know.

Sir I also used bsmap, but not getting way to determine methylated C percentage,
In many paper they are using Binomial approach to calculate methylated C, In which total no. of methylated and non methylated reads are required,
So my question is, how to calculate no. of methylated and non methylated reads.
plz help