Filtering out relevant Gene-fusions
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8 weeks ago
soniabedi.07 ▴ 10

Hi. I performed STAR-fusion for obtaining Gene fusions from my sample (human). I got a high number of gene-fusions. I suspect there might be some noise in the results I obtained. Is there way to filter out actual relevant gene-fusions from my data? What criteria should I be looking out for?

Thanks in advance.

Gene fusion filtering • 145 views
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7 weeks ago

Fusion events are largely affected by how well the mapping happened at the junctions/break-points. Consider the following :

[1] Was Star-Fusion executed with --max-sensitivity option; if yes, try disabling and rerun.

[2] Check the output file. Those predictions that have very few JunctionReads and/or SpanningReads are going to be enriched for false positives. Note, depending on the site of the fusion breakpoint and length of the reads, it may not be possible to have SpanningFragments and all evidence may show up in the form of JunctionReads.

The JunctionReads column indicates the number of RNA-Seq fragments containing a read that aligns as a split read at the site of the putative fusion junction.

The SpanningFrags column indicates the number of RNA-Seq fragments that encompass the fusion junction such that one read of the pair aligns to a different gene than the other paired-end read of that fragment.

source: https://github.com/STAR-Fusion/STAR-Fusion/wiki

[3] Try using other tools; here is list - Gene Fusion Detection: Rna-Seq Data

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