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Hi,
I am working with RNA-seq data to identify gene fusions. I'm currently using fgbio for UMI grouping and consensus sequence calling.
As well as using the tools in the latest fgbio release to …
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[Here](https://github.com/cancervariants/metakb/issues/66#issuecomment-815096876), we can see that the variant normalizer is unable to normalize `delins` and `del` HGVS queries.
> NP_001333827.1:…
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Hi,
I am attempting to annotate a customized VCF file using NCBI's GFF and (fna) FASTA files for the Newcastle disease virus (https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_004786615.1/). However, …
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We can probably leverage KBs and PeCAN datasets to separate LoF genes vs variant hotspots for this list.
This will be more relevant than just a list of gene symbols.
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Hi, I am just wondering if there is a recommended QC steps that is recommended for input bams?
For e.g. recommended MAPQ threshold for minimap, removing supplementary reads, etc. ?
Thanks,
Sowm…
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Reactome
http://amigo.geneontology.org/amigo/gene_product/UniProtKB:P62979
http://amigo.geneontology.org/amigo/gene_product/UniProtKB:P62987
About 90 annotations for both spanning many processe…
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Hello,
I used the STAR-Fusion v1.9.0 to built my genome lib with prep_genome_lib.pl, but no matter what version genome I used, all of them reported the following errors:
**died with ret 9 No such…
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Systematic ID | Gene name | Product description | Budding yeast orthologs | Human orthologs | Targets
-- | -- | -- | -- | -- | --
SPBC115.02c | afg1 | AFG1 family mitochondrial ATPase/chaperone Afg1…
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Current SBOL RNA-related glyphs (i) do not capture the range of RNA functions and (ii) where they do exist are not expressive enough to precisely annotate the RNA function. A new set of glyphs that mo…
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@edrill suggested this. This can be useful for oncoprints and more in-depth mutation specific analyses.
The relevant information seems to be in the following MAF columns:
``` r
table(gnomeR::…