Kmer size in Kallisto Index

[Anupriya014]

Hi all. I want to test out the --long parameter in Kallisto bus. For this, I need long reads FASTQs (oxford nanopore may be) and index (.idx file) from Kallisto index ran with k-mer size of 63? What if I generate index with 31 kmer size for long reads?

Also, I will be testing Quant. So, please tell me optimal settings for it as well. Sorry, if these questions sound very naive as I am new to Kallisto.

Thanks!

[Yenaled]

Yes, 63 for index k-mer size.

And you can use --long and --platform=ONT when running pseudoalignment.