"MethylKit" package for WGBS data

Question

[shrinka.genetics]

Hi I am working with WGBS data, There I am using MethyKit package. Generally it takes input file containing a strand information column. Anyone can tell me that whether it can work on a file which does not contain any strand information?

Thanks Shrinka

Answer 1

[Papyrus]

I've used it for RRBS data which I had previously preprocessed to remove strand information. So at least it can work with files in the bismarkCytosineReport format with no strand info, indicated by *:

1 10484  *  0  5 CG CGG
1 10489  *  5  0 CG CGC
1 10493  *  0  5 CG CGC
1 10497  * 82  4 CG CGG

by reading them with the methRead function with the argument pipeline = "bismarkCytosineReport".

[shrinka.genetics]

Thanks for your reply. Could you please tell me that

1) Output of Bismark aligner doesn't contain strand information? I presume your aligner was BISMARK and you have put "*" in the place of strand information. Please correct me if I am wrong

2) Are the nos in column 3 and 4 position depicting No of converted Base and No of Unconverted Base or vice versa?

I am waiting for your reply

Regards Shrinka

[Papyrus]

1) Yes, it does contain strand information. I preprocessed the data myself, outside of methylKit, to collapse by strand the measurements (I did not simply substitute strand information for "*").

2) As you can see in the Bismark User Guide the cytosine report format is as follows:

chromosome | position | strand | count methylated | count unmethylated | C-context | trinucleotide context |

(I edited the previous answer because the chromosome column was missing)