I have a question about these two arguments for the BSSeeker2 methylation calling step:
-x, --rm-SX Removed reads with tag 'XS:i:1', which would be considered as not fully converted by bisulfite treatment [Default: False] --rm-CCGG Removed sites located in CCGG, avoiding the bias introduced by artificial DNA methylation status 'XS:i:1', which would be considered as not fully converted by bisulfite treatment [Default: False]
Both of these seem to be removing false positives from the results, which seem like a generally good thing to do, but their default value is "False". Usually the defaults for a program are calibrated to the most general use case, but I'm not sure if that's the case here. Is it standard practice to use these arguments? Why would I want to not use these?
I have RRBS data, not WGBS, if that makes any difference.