Once you finished the methylation extraction you can simply take the C-context output and simply concatenate it, e.g.
cat CpG*.txt > CpG_context_merged.txt
or
zcat CpG*.txt.gz > CpG_context_merged.txt
and use this merged output as input for bismark2bedGraph. The only thing that is somewhat inconvenient is that you don't get one nice mapping report / html file because the alignment process was split up into 3 processes...
cat CpG*.txt > CpG_context_merged.txt
or
zcat CpG*.txt.gz > CpG_context_merged.txt
and use this merged output as input for bismark2bedGraph. The only thing that is somewhat inconvenient is that you don't get one nice mapping report / html file because the alignment process was split up into 3 processes...
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