Kallisto for RNAseq

Model Organism: Worms Methods & Reagents
1

Has anyone tried Kallisto/Sleuth with worm RNAseq data? If so what source did you use for your transcriptome index?

Thanks

2

I used Kallisto for my mRNAseq data, about a year ago. My transcriptome index was from:

ftp://ftp.wormbase.org/pub/wormbase/releases/WS252/species/c_elegans/PRJNA13758/c_elegans.PRJNA13758.WS252.mRNA_transcripts.fa.gz

There are more recent wormbase releases you could use instead (WS258). Kallisto is amazingly fast at quantifying reads!