Removing fused transcripts from RNA seq data
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.
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Some tools may be old but take a look at this: Gene Fusion Detection: Rna-Seq Data