Comments (6)
@slowkow I agree, that piece code is challenging, with multiple levels of redirection and bit encoding!
My guesses are:
- ts transition ie. adacent A<=>G or C<=>T
- tv transversion - the other possible [AGTC]<=>[AGTC] ajdacent pairs
- CpG CG pair (revcom aware)
- CpG-ts CG pair (revcom aware) but allowing transitions in 1st (and/or 2nd) base
- 2 number of ambiguous IUPAC bases with 2 possibile values
- 3 ditto with 3
- 4 ditto with 4 (I assume this means "N")
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@tseemann Thanks for the helpful explanation! Your explanation sounds correct to me.
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And what's the parameter "-u" meaning?
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@pengchy According to the code, -u
means upper_only=1
and it seems to only count uppercase letters in the composition statistics ie. it masks all lowercase letters.
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Thank you @tseemann, It is very helpful.
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👍
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