Kallisto --fusion detection single reads

[FabianGrammes]

Hi I have a data set of (100bp) single-end RNAseq reads. I would like to look for gene fusions (with pizzly afterwards) so I'm running:

kallisto quant -i MyIndex --fusion --single -l 350 -s 40 -o MyOutput My.fastq.gz

The -l and -s parameter are deduced from the BioAnalyzer traces. Kallisto (version 0.43.1) runs without complains, but all the fusions.txt files are empty (containing only the header line). So my question is:

• Can kallisto call fusions from single end reads
• If yes, then what am I doing wrong. I've run kallisto on 52 samples and all fusions.txt files are empty.

cheers, Fabian