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Hello,
I have been using Docker build of OptiType for my project, and am satisfied by its performance.
One concern is that it always use reference sequence & alleles in /data folder of the Docker im…
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Hi all,
I run
```
user% ./NERVE.sh -epp False -vir True -rz True -p1 UP000000625 -wd /Users/ab/Applications/NERVE/docker/nerve/workdir/ecoli -g n -m True
```
and got :
```
wrote config …
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Hi, can SpecHLA type DRB3 and DRB5 as kourami? Thanks
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I am trying to use this tool to predict whether a specific CDR3b sequence binds to an antigen. However, when I run the pedict.py with just this information, it throws an error. I don't have MHC or H…
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Hi there,
I am trying to integrate a newer version of the IMGT Database for my analysis but there seems to be an issue at the DRB1 locus. I downloaded the database from: ftp://ftp.ebi.ac.uk/pub/data…
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I noticed that the collaborators are using the somatic VCF files to look for somatic mutations in the HLA genes. These genes are known to be problematic for alignments to the human reference genome si…
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hisatgenotype doestn't works if HLA sequence files from the repo are substituted to new ones from IMGT-HLA database (version 3.30.0)
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Hi,
Thank you for this great tool.
Can HATK outputs the logistic result, Manhattan plot and heatmap result based on Pgroup/Ggroup?
I noticed that it has --Pgroup/--Ggroup parameters in HATK.py.
…
jpgsu updated
3 years ago
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Using the docs: https://pygfe.readthedocs.io/en/latest/readme.html I'm unable to run through the example code.
Building and running in local python 3.7 env.
```
from Bio import SeqIO
from Bi…
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Webservice that chooses a reference sequence based on
Input:
1) HLA (or other) consensus sequences. full length or features.
2) IMGT version.
Output:
1) Best matching reference sequence
2) …