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### Installation Type
Docker
### pVACtools Version / Docker Image
Docker container, version 4.4.1
### Python Version
_No response_
### Operating System
_No response_
### Descri…
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Hi. i have provided the two different alleles in my reference sequence. however, i'm not sure if kallisto can handle this properly. also, what happens in the case of homozygosity? is the tpm reported …
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Hello,
Thank you for developing this nice tool.
I'm interested in analyzing allele-specific expression (ASE) in my single-cell RNA-sequencing (scRNA-seq) data. This data comes from offspring tissues…
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Hello,
I ran phASER for multiple samples and extracted allele specific expression for each sample independently.
Seen that these samples are split into case/control, I would like to process these …
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**[Original report](https://bitbucket.org/whatshap/whatshap/issue/169) by Irantzu A (Bitbucket: [iraun](https://bitbucket.org/iraun), ).**
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Is it possible to …
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Hi,
I am a new user of the `coloc` package and need clarification on how to correctly set up input parameters, particularly `MAF`, `N`, and `sdY`. I am working with GWAS and eQTL data, where the GW…
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**Transferred from:** [NIF-11599](https://support.crbs.ucsd.edu/browse/NIF-11599)
**Original Reporter:** Nicole Washington
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We need a section of GENO that records the properties of an "allele" on…
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Hi,
If it’s possible to add both gene and transcript expression annotations to the input VCF file for `pVACseq` (`GX` and `TX` fields with `vcf-expression-annotator`), is it advisable to include bo…
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Hello,
I'm having trouble installing alntools. I followed the instructions on the GitHub page (https://churchill-lab.github.io/alntools/), but I'm encountering an error when trying to run the tool.
…
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Hi,
I am trying to count allele specific expression from RNA-seq data, beacuse I am working with specific cell model, I am not have paired SNV infomation, is it feasible to use population-level SN…