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seq comp documentation per #47 #181

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seq comp documentation per #47 #181

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12 changes: 12 additions & 0 deletions README.md
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Expand Up @@ -59,3 +59,15 @@ Seqtk Examples

seqtk trimfq -b 5 -e 10 in.fa > out.fa

* Report the composition of the sequences in `in.fa`:

# Output format: chr, length, #A, #C, #G, #T, #2, #3, #4, #CpG, #tv, #ts, #CpG-ts
# where A, C, G, T is counts of individual nucleotides,
# #2 describes IUPAC bases with 2 possible values
# #3 describes IUPAC bases with 3 possible values
# #4 describes IUPAC bases with 4 possible values (N)
# #CpG CG pair (revcom aware)
# #tv transversion - the other possible [AGTC]<=>[AGTC] ajdacent pairs
# #ts transition ie. adacent A<=>G or C<=>T
# #CpG-ts CG pair (revcom aware) but allowing transitions in 1st (and/or 2nd) base
seqtk in.fa