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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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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,
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…
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I am using version 2.4.0 of Arriba and I stumbled across this error:
```
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[2024-08-24T15:53:20] Reading chimeric alignments from '~/bams/sample1_trimmed.star.hg38.Chimeric.bam' (total=138010)
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Hello,
Thanks for developing this tool! I was testing it on some hematological samples with TCF3 gene fusions (confirmed by FISH), and it seems like GeneFuse is not picking them up. I have checked th…
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Found that starfusion will occassionally output more or less fusions, or output the same breakpoint but report differing gene names and gene ids for the same sample.
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Hello! I am using STAR-Fusion to generate fusion transcripts for the RNA-Seq data of _Arabidopsis thaliana_
**I have first used the Ensembl Plants 51 (latest) version of gtf file and I could not ev…
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Hi,
After running svtyper, in the VCF file there are DPs in the INFOs. May I ask how the depths are given since when I checked manually the depths very a lot around the breakpoints, especially when…
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Thanks for creating this tool! I have noticed that the `scripts/make_fusion_genes.py` reports wrong order of exons for genes in '-' orientation, which results in considering some fusions as untranscri…
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amar@amar-Virtual-Machine:~/GeneFuse$ ./genefuse -1 testdata/R1.fq -2 testdata/R2.fq -r Homo_sapiens_assembly19.fasta -f genes/cancer.hg19.csv
22:53:5 start with 4 threads
22:53:9 mapper indexing d…