Question: Should I remove incomplete bisulfite conversion in the BSSeeker2 call step?
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gravatar for colin.kern
4 months ago by
colin.kern780
United States
colin.kern780 wrote:

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.

rrbs methylation • 147 views
ADD COMMENTlink written 4 months ago by colin.kern780
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