Entering edit mode
3.5 years ago
shrinka.genetics
▴
40
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
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
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:(I edited the previous answer because the chromosome column was missing)