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Hi Brian,
I recently tested the CCLE K562 cell line with STAR-Fusion run to test for BCR-ABL1 fusion. However, the final fusion output contain no fusion genes. The run looks ok, I find no error rep…
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Hello Dr. Dobin,
I am optimizing the options of STAR to detect fusion genes, and have two questions.
1. Unmapped reads in 'Chimeric.out.junction'
The unmapped reads with STAR are mapped in Chi…
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Hi,
I have Arriba fusion caller results (run with Gencode v27 equivalent to Ensembl 90) and wanted to test the following `out-of-frame` fusion:
#gene1 | gene2 | strand1(gene/fusion) | strand2(ge…
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Hi
So I am not exactly working human genomes at the moment but rather a set of synthetic fusions designed to mimic fusion genes. How it works is we generated an in silico chromosome, rearranged it…
dwooi updated
3 years ago
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Hi sigven,
The "fusion" evidences providing function is not added to the PCGR (v0.9.1) we are using, so we develop and use our own script to provide the evidences.
Could you tell me how you plan…
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Dear,
Currently, we detect most of our expected fusions using starfusion software.
However, for one sample, a MET exon 14 skipping (resulting in a fusion between exon13 and 15) is expected.
A s…
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Hello!
It is a question rather than an issue.
STAR is a very good aligner with its great performance and the configurable options for users to control mapping in detail.
I use STAR and STAR-Fusio…
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The following improvements for the Mutations/Fusions/CNAs comparison tab were proposed by @jjgao and @tmazor in cBioPortal/cbioportal#8107:
- [ ] (item 8) Make Mutation, Fusion and CNA types in men…
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Hi,
I'm running STAR-Fusion v1.8.1 via Singularity with the command:
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singularity exec ~/star-fusion.v1.8.1.simg \
/usr/local/src/STAR-Fusion/STAR-Fusion \
…
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Hi,
We're trying to call fusion transcripts in cervical cancers with HPV, using a reference we created by adding various HPV strains to hg38. When we run LongGF on data aligned to this reference, u…