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e.g. B2M, TAP, &c.
Identifying loss in MHC might require running a custom program which first does genotyping of the germline MHC and then calls somatic variants against those specific alleles.
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The Protein Ontology has been tasked with taking over the protein-related terms from MRO (Major Histocompatibility Complex (MHC) restriction ontology). The MRO terms are often defined with respect to …
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Convert the workflow [allele-specific-expression](https://github.com/icgc-argo-workflows/allele-specific-expression) to follow `nf-core` structure and guideline.
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Hey, I am trying to do allele-specific expression analysis (ASE) for a few RNA seq samples ( 32 disease and 5 normal samples, unpaired unrelated). Could you suggest a pipeline/method to convert the ma…
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The current definition of 'variant collection' in SO is “a sequence collection comprised of one or more sequences of an individual”.
A. It is not clear what is meant by ‘of an individual’ . . . this s…
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Hi,
I am intersected in a region in chr6 and I only have the SNP information in this region. Can I used the allele-specific mode to study the differences of contacts between two alleles in this regi…
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There's no documentation I can find about how kallisto handles mismatches to the reference transcriptome. Is there any way to set a maximum value or to quantify the mismatches, such as for the purpose…
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Hello,
I have a more methodological question - I am dealing with a partially collapsed diploid plant genome assembly.
I did my phasing using 10x data (see issue #262) but now I realized that most …
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The VCFs generated by QDNAseq do not conform to the specification for the reference allele field, as they contain symbolic alleles e.g. ``. This results in errors when trying to either validate the VC…
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Hi,
I am currently benchmarking tools that balance "compression and accessibility" for genotype data and encountered an issue when using XSI with large datasets. I hope you can assist me in resolvi…