kallisto K-mer size

Question

[rahmati.razieh83]

Dear every one

I have a fasta denovo assembled file provided by trinity with the kmer size=25. I want to make quantification by Kallisto but the kmer size of kallisto is 31by defaulte. Is it necessary to change the K-mer size of kallisto to 25 or I can use kallisto with the kmer size=31? If it is better to I change the Kallisto Kmer size to 25, how can I do this work and How can I change the Kallisto Kmer size? Thanks in advance

Answer 1

[Devon Ryan]

You don't need to change the kallisto k-mer size just because you used a different one during the assembly.

For what it's worth, setting the k-mer size in kallisto is done during indexing with the -k option.