Removing fused transcripts from RNA seq data

Question

[Max Ivon]

Hello! I have performed alignment of paired-end data with tophat with the following options:

tophat --no-coverage-search --max-multihits 1 -p 4 -o <...> <...> <...> -G <...>

What would be the easiest way to remove read pairs coming from fused transcripts based on annotation provided with the "G" options?

Thanks in advance.

[GenoMax]

Some tools may be old but take a look at this: Gene Fusion Detection: Rna-Seq Data