brianjohnhaas
commented
8 months ago Hi,
The fusion isoforms are based on the fusion transcript breakpoints, and so the specific exons that are spliced together in the fusion transcript. The expression values are estimated based on the number of reads that support that specific breakpoints.
If the --predict_cosmic_like returns NA, then it means that it's not finding it as either cosmic-like or as a type of artifact - so just an ordinary fusion transcript. I wouldn't consider it low confidence, it's just that it's not strikingly similar to other known biologically relevant fusion transcripts wrt to its features.
Hope this helps,
Brian
On Thu, Jan 25, 2024 at 4:49 AM giulialopatriello95 < @.***> wrote:
Hi there!
I would like to validate experimentally some fused genes. For doing that, I should keep the most expressed isoform for each gene. I would like to know how FusionInspector decides the isoforms of the 2 patner genes. Are these the canonical isoforms or are the most probable ones with highest expression (as it seems from your pubblication)?
In addition, running --predict_cosmic_like parameter, some results are reported as "NA". Should I consider these results as low confidence results? If not, are these still valid results?
Thank you in advance, Giulia
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Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas
Hi there!
I would like to validate experimentally some fused genes. For doing that, I should keep the most expressed isoform for each gene. I would like to know how FusionInspector decides the isoforms of the 2 patner genes. Are these the canonical isoforms or are the most probable ones with highest expression (as it seems from your pubblication)?
In addition, running --predict_cosmic_like parameter, some results are reported as "NA". Should I consider these results as low confidence results? If not, are these still valid results?
Thank you in advance, Giulia