Explain seqtk comp columns

[slowkow]

The usage says:

seqtk comp
Usage:  seqtk comp [-u] [-r in.bed] <in.fa>

Output format: chr, length, #A, #C, #G, #T, #2, #3, #4, #CpG, #tv, #ts, #CpG-ts

Can you please explain the meaning of #2 #3 #4 #CpG #tv #ts #CpG-ts? I read your code, but it is hard to digest for me.

[tseemann]

@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")

[slowkow]

@tseemann Thanks for the helpful explanation! Your explanation sounds correct to me.

[pengchy]

And what's the parameter "-u" meaning?

[tseemann]

@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.

[pengchy]

Thank you @tseemann, It is very helpful.

[tseemann]

👍