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Dear Sirs,
I am trying to make HLA Genotyping for HLA-A, HLA-B, HLA-C, HLA-DRB1, HLA-DRB2 and HLA-DQA1. Please tell me where can I find the HLA reference files in VCF format, as it is required for …
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Great idea to make this a separate tool, I've found a need for MHC parsing outside of prediction as well.
For class II alleles with alpha/beta chains, NetMHC requires them to be entered as paired all…
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Hi hista-genotype folks,
Our group is very interested in your software to determine the haplotypes of patient samples.
We sequenced the HLA-A and HLA-B loci.
When we run your software it typical…
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run command:
hisatgenotype --base hla --threads 4 --bamfile SRRxxxxxx.bam
BAM file is generated previously by STAR 2.7.0
--------------------Python error trace message:
Traceback (most recent cal…
nikyk updated
2 years ago
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Hi @cdarby
Thanks for making this tool! I'm having some trouble interpreting the outputs, and I'm hoping you can help.
So I've run the pipeline twice now on two different 3' scRNA-seq PBMC data…
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If the HML is from a donor recruitment lab, there will be a Property element under Typing which will contain a name of SupplierOrderLineID and value with an id. Use this to create ProcecureRequest (ST…
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Dear Pascal,
I have got the error message likes the following when I used _parseHLADbAlignment_ function, can you give me some advice on how to avoid this error message?
I'm looki…
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The multiple sequence alignments in the `data` folder are almost 2 years old. Since then, many new alleles have been discovered and recorded in IMGT/HLA and existing alleles have been renamed or impro…
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Update https://github.com/lgragert/srtr-impute-pubsaf2306/blob/main/aa_mm_biopython_runmatch_genie_9loc.py to assign AA-MM for the full protein
Determine where the full protein starts for each loc…
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### Description
As a user, I want to understand the usability of models based on additional markers, such as
tumor mutational burden (TMB)
The total number of mutations (changes) found in the DNA of…