coverage2cytosine

[ShouWenWang]

Hi, Felix
I have some trouble with coverage2cytosine... I am using the code:
coverage2cytosine --nome-seq --genome_folder genome_folder -o report input_data.deduplicated.bismark.cov.gz

I had expected the CpG reports to contain only the context of ACG and TCG, but this is what I get:
1 34741246 - 1 0 CG CGC
1 35403302 - 1 0 CG CGG
1 35403394 - 1 0 CG CGG
1 36471854 - 0 1 CG CGA
1 36471885 - 0 1 CG CGA
1 36471891 - 0 1 CG CGG
1 36471936 - 0 1 CG CGC
1 36471966 - 0 1 CG CGG
1 36471975 - 0 1 CG CGT

Also, I had expected the GpC reports to contain only the context of GCA, GCT, GCC, but this is what I get:
1 4445691 - 0 1 CHH CCA
1 4445750 - 0 1 CHH CCC
1 4523988 + 0 1 CHH CCC
1 4523994 + 0 1 CHH CAT
1 4523999 + 0 1 CHH CCT
1 4524014 + 0 1 CHH CTA
1 4524034 + 0 1 CHH CAA
1 4524044 + 0 1 CHH CTA
1 4524054 + 0 1 CHH CAA
1 4524066 + 0 1 CHH CAT
1 4548184 - 0 1 CHG CTG
1 4548197 - 0 1 CHG CTG
1 4548224 - 0 1 CHH CCT
1 4548227 - 0 1 CHG CTG

What is going on here? How can I get a report that I had expected...

[FelixKrueger]

Hi @ascendancy09

To be honest, so far there is nothing that looks weird to me. For CpG reports, only CpGs in the context of ACG and TCG are shown, however the format of the CpG report only shows the downstream context, but not the upstream base (which I would expect to always be A or T).

In a recent issue (#321) we have added a cytosine context summary which is now always printed when you run coverage2cytosine. This report does report the upstream base, so it should be able to see the GpC methylation in there. If you would clone the current development version (a release is due probably next week or the week after), you should benefit of this report.

For the GpC reports, you more or less want to see any context but not CG, which seems to be exactly what you got. Again, here the upstream base does not show in this report, but if you would check in a genome browser you should see that each C is preceded by a G, hence, GpC methylation.

I hope this clears things up?

[ShouWenWang]

Thanks! Now it makes sense to me!

[FelixKrueger]

Excellent, best of luck!