I'm trying to find a way to convert a GEO WGBS data set into a methylKit-workable form. I've used methylKit for ERRBS data in the past but this data set has very different formatting. This data was processed by the authors with Bismark methylation extractor and is in a txt file. It looks like one of the files is sorted and the other one isn't but it's hard to understand exactly what processing they did. From doing some reading it looks like the data needs to be in a sorted SAM or BAM file format in order to use processBismarkAln in methylKit. I'm not familiar with Bismark and I haven't used Perl very much. Does anyone have any advice as to how to convert it based on it's current form? Does anyone have an example of the SAM file format that will work with with processBismarkAln?
This is the first data set:
The second file: