alignment strategies for rna fusion

Question

[from the mountains]

I'm wondering what is better for detection of fusion events in RNA seq data: global or local? i am trying to decide between --end-to-end and --local modes in bowtie2

[ATpoint]

You need a dedicated tool to detect fusion events in RNA-seq. Please google for tools or use the search function here and then use the alignment tool and parameters that the fusion detection tool recommends.