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Hi,
I am running into an issue with the HLA typing that I cannot figure out. The program fails with the message:
Traceback (most recent call last):
File "bin/optitype_ext.py", line 31, in
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- **Workflow changes**
- [x] Sample name as workflow parameter for better output dataset naming
- [x] PEAR
- [x] give percentage along with count
- [x] adapter clipping (Cutadapt)
- [ ]…
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Hi!
Is there a chance it will work with long reads like Nanopore or Pacbio?
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Hi, I wonder if I could feed the bed, bim and fam files output from SNP2HLA into HIBAG to get the HLA class I and II typing.
Thank you in advance!
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Hi! I'm running long_read_typing.py for PacBio -reads for which I have extracted the HLA-regions (originally aligned data to chm13, then extracted hla with HLA*LA and ran bam2fastq). I was wondering a…
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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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Replicate the Germline Exome & HLA typing stepwise on AWS and record documentation on Google doc.
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Hi,
I'm running some samples through HLA*LA and I've been hit by this error.
```
Extract reads from 1 regions...
Extract unmapped reads...
[main_samview] fail to read the header from "-".
Ex…
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Hello
I'm trying to use polysolver to do HLA typing from exome data.
What does it means if I get 'winners.hla.nofreq.txt' instead of 'winners.hla.txt'?
I always get this filename as final output …
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Hi
I'm facing this error:
`Have found no compatible reference specifications in /nemo/stp/babs/working/barriop/.conda/envs/HLA_typing/opt/hla-la/src/../graphs/PRG_MHC_GRCh38_withIMGT/knownRefere…