Removing fused transcripts from RNA seq data
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4.0 years ago
Max Ivon ▴ 120

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.

RNA-Seq • 833 views
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Some tools may be old but take a look at this: Gene Fusion Detection: Rna-Seq Data

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