diff --git a/README.md b/README.md index 6dec1cc..50eca32 100644 --- a/README.md +++ b/README.md @@ -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