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Hi
I have downloaded a few TCGA chr6 bam files which after converting them to fastq I've run in Optitype (docker version). I've used WXS and RNA for the available sample types (normal tissue, norma…
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Hi, I am using optitype for HLA typing, thanks for developing such a wonderful tool!
I firstly use razers3 and samtools to extract the reads mapped to hla genes(zero step), and then use OptiTypePipel…
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I'm running Optitype in docker. Is there any way to keep the aligned bam to reference HLA fasta? I think its created as intermediate file, and I would like to keep it.
Not sure how to modify the co…
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Hi,
I'm running optitype in rna mode for fastq.gz files. I get a large cryptic error that I'm not really able to figure out. Can someone help me translate this? See the command and error below:
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ghost updated
6 years ago
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after using upgrade -u development had a similar behavior as to #2136 and i used the same procedure to debug
i got this error:
```
root@cbc6fb3a9444:/tmp/opti# OptiTypePipeline.py -v --dna -o t…
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The following code below was modified in main.nf.
Simply removed the unzip process and replaced with modified yara mapper script.
The code was run as follows:
`nextflow run ~/nf_scripts/hlaTy…
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Hi,
Is there anyway for OptiType to take bam files directly without having to run bam2fq?
Thanks,
-todd
ghost updated
6 years ago
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Hello,
I want to ask for help about how to speed up the pvacseq computation.
I use `NetMHC` method, `9` epitope length and all valid HLAs for `NetMHC` method, it costs about 1 hour to finish a s…
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prateek@cpu:~/dhwani$ sudo docker run -v test:/test -t fred2/optitype -i NA11995_SRR766010_1_fished.fastq NA11995_SRR766010_1_fished.fastq -d -o out
sudo: unable to resolve host cpu: Connection timed…
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I have 4 sets of patients, each has a normal, primary, and metastasis
I use a template to call variants on these, and have a csv file which looks like this:
```
samplename,batch,phenotype,varia…