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Here are all the genotype comments, with links to the genotype pages: [genotype_comments.txt](https://github.com/pombase/website/files/14771447/genotype_comments.txt)
Here are some examples:
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Hi all,
I am trying to do genotyping (DNAseq samples) and allele specific expression (RNAseq samples) of a recently assembled plant (alfalfa (Medicago sativa L.)), [nature paper here](https://www.n…
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cc @ValWood @kimrutherford
What can we do nowadays to curate results from gene expression in a given mutant (over / under expressed transcripts)? A phaf file? I can imagine that certain genes will …
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For some of our analyses it would be helpful to be able to filter a VariantCollection to only those variants that fall within the intended capture targets.
Example intervals list:
```
[odonnt02@mine…
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Hi there,
since GDC release 23 there is a new readout for TCGA, 'Allele-specific Copy Number Segment'. It would be great if it were downloadable in TCGAbiolinks via:
```R
query.cnv = TCGAbiolin…
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Seems that there have been discussions/ideas happening about genotype/variant representation - with use cases/requirements coming from Monarch and other efforts (e.g. JAX, MGI, MPD, AGR, etc).
I'd …
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Hi, would it be possible to have `split_multiallelic` also adjusting the table schema?
I know this implies some work to also adjust every other method that assumes arrays due to multi-allelic prope…
Hoeze updated
4 years ago
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Hi
I'm using this tool and I noticed that it supports implicit phasing. Could you please clarify how implicit phasing differs from the standard (explicit) phasing? Additionally, is it possible for …
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PHI base would like to be able to specify (in some cases), the methodology of the allele creation, as it can affect the expression level
The example provided was "promoter knockdown" vs. RNAi. Thi…
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I've successfully run the example. I don't understand the output
out/merged_snp/jurkat_chr1/final.tsv.gz
What is the final call? And is what should I use as the measure of confidence?
Thank…