Question: kallisto K-mer size
0
gravatar for rahmati.razieh83
22 months ago by
rahmati.razieh8330 wrote:

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

alignment • 1.1k views
ADD COMMENTlink modified 20 months ago by Biostar ♦♦ 20 • written 22 months ago by rahmati.razieh8330
0
gravatar for Devon Ryan
22 months ago by
Devon Ryan92k
Freiburg, Germany
Devon Ryan92k wrote:

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.

ADD COMMENTlink written 22 months ago by Devon Ryan92k
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