Anyone know the best (or recommended) kmer size to use with sailfish and Arabidopsis thaliana RNA-seq data?
Background: To use sailfish, you first must create a transcript index using a fasta file of your transcripts. To make the index, you need to pick the kmer size.
Also if anyone needs a copy of Arabidopsis transcript fasta sequences let me know. I can give you the same for other plants if you want. It's very easy using getFasta from bedtools and a few other CL utilities.