Closed jmattock5 closed 1 year ago
Hi, Sorry for the late reply. In kmtricks, k-mers are always represented in canonical forms. Did you try to grep the reverse complements of the missing k-mers? Note that kmtricks computes canonical form according to this alphabet order: A < C < T < G. Teo
Hi, With this info of the alphabet order kmtricks uses I was able to find the canonical kmers in my fastas, problem solved. Thanks! Jenny
Hi, thanks for making this great tool! I'm trying to generate kmer presence/absence matrices with these commands:
kmtricks pipeline --file list_five --run-dir output_5 --cpr --mode kmer:pa:bin
kmtricks aggregate --run-dir output_5 --pa-matrix kmer --format text --cpr-in --sorted > output.txt
I've noticed that, in the output, kmers are being reported as present in an assembly but when I grep for that kmer it isn't in the fasta. Are there any settings I can use to prevent this happening? I've tried
--hard-min 1
which didn't help.Thanks! Jenny