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Annotation for balanced structural variants is messy at the moment; e.g. an inversion will show a lot of genes between the breakpoints with all kinds of functional annotations, like start_lost etc as …
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Hiya,
Can Arriba be used to detect fusions in single-cell RNAseq data (e.g. Smart-seq2). I expect to see a greater number of false positives compared to bulk RNAseq, and with a lower number of read…
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Hi there,
I apologize for the naive question I'm about to ask, but I've been struggling with this for a week and would appreciate some help. I created a custom gene index using a FASTA file of fusi…
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Systematic ID | Gene name | Product description
-- | -- | --
SPBC56F2.09c | arg5 | arginine specific carbamoyl-phosphate synthase subunit Arg5
SPAC25G10.02 | cce1 | cruciform-cutting endonuclease…
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from what i can tell, only one of the two genes in a gene fusion is curated in oscar's database. for example, selection of therapy_variant.id = 724 gives:
+--------------------+--------------------…
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Hi there,Do I need full-length transcripts to use ESPRESSO? For example, if the reads are not full-length, do they need to be filtered out?
Why do different positions of the same transcript support d…
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Hello @lakigigar and co-developers,
we're currently running @chapmanb's [bcbio](https://github.com/chapmanb/bcbio-nextgen) in production for quantitating RNA-Seq expression and calling gene fusion ev…
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#### What data file(s) does this issue pertain to?
`fusion-annoFuse.tsv.gz`
#### What release are you using?
v13-v15
#### Put your question or report your issue here.
Per the comment …
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Thanks alot for the apprecitated tool
I have applied JAFFAL for a single cell long read nanopre data and it works nicely in both the healthy and mutation samples.
What I want to do now is to det…
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The pipeline filters genes were one of the genes is not in the gene-list. This may miss some fusions of interest.