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Hi
I know somebody down here had the same problem.
I'm trying to use optotype in docker:
`docker run -v /local/pVACtools/:/data/ -t fred2/optitype --input SRR2672972_1.fastq SRR2672972_2.fastq …
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Hi there,
I know this particular error has come up a few times now on different issues (e.g. https://github.com/FRED-2/OptiType/issues/66), but I believe I have taken all the steps mentioned in the s…
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Hello @lkuchenb ,
I wanted to ask if this tool can handle fastq reads from Nanopore or PacBio. With a different aligner I can run xHLA and HLA-LA. My question is mostly about Optitype. Will it be a…
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Hi~ Thank you for this wonderful work, i would like to know about an issue i came across.
KIR3DL3, KIR3DP1, KIR2DL4, and KIR3DL2 are four frame kir genes which in principle every individual should h…
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https://github.com/namphuon/ViFi
Docker image and Dockerfile is there.
I think this tool makes more sense than GENE-IS; we're investigating if there are differences.
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```0:00:00.63 Mapping test.fastq to NUC reference...
Failed to open genome file /usr/bin/data/hla_reference_rna.fasta
Exiting ...
Traceback (most recent call last):
File "/usr/bin/optitype", line…
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I know someone put a similar error before, but my case is a little bit different:
Since our cluster doesn't have docker, I have to use another container-based software Singularity, theoretically it…
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Hi,
Thank you for developing the great tool! I have been using Optitype v1.3.2 and recently switched to the latest version, v1.3.5. Interestingly, all the samples that were used to successfully f…
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### Description of feature
Hello.
Because all typing tools have their limitations & advantages (datatype, reads length, read depth, resolution, type of genes typable, etc.), it could be interestin…
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I'm using optitype/1.3.1, specifying solver=cbc in config.ini, using hla_reference_dna.fasta. i prefilter my reads using razers3. This is the output i'm getting with my own data.
```
A1 …
kylec updated
4 years ago