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Hi,
Thank you for this tool, I tried the pipline you provided on my data, but during denovo detection, I got a lot of warning:
2024-11-24 20:55:02 [WARN] - Skipping invalid data in M
2024-11-24 20:…
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Hi,
I used clairs(v0.4) to call somatic SNV/InDel(tumor/normal paired), but the PASS variants number is ~6w. Is it normal?
Compare to deepsomatic, the somatic SNV/InDel number is ~1.7w.
Do you …
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I have an issue loading a previous session from a session xml file.
In a previous session, I changed the track height and set track colors to correspond to their conditions. However, when I reload …
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**Describe the bug**
I am trying to generate synthetic bam file using NEAT and it crashes with error "AttributeError: 'NoneType' object has no attribute 'reference_id'".
**To Reproduce**
That's …
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My experiment consists of six samples divided in two groups. I want to carry out RiboDiPA analysis, but I got an error related with p-site mapping:
`Computing P-site offsets`
`Computing coverage…
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Hi,
I was wondering if I would like to calculate coverage across the genome for specific window size (ex. 100kb) using a BAM file, do I need to supply a reference genome file when I run PathDepth? Or…
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Hello,
Thank you for making this program.
I am hoping to resolve some haplotype switch errors in my regions of interest, and I think Methphaser would be very nice to try out.
My regions of int…
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Hello! We were looking at the exon counts again and saw some discrepancies from what we expected. This one comes from reads going on one strand counting as being excluded from the gene on the opposite…
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### Feature Request
To help streamline our QC notebook, we can rely on the samtools coverage output to quickly check the coverage of the 69/70 deletion instead of opening up each bam file; however si…
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Hello...
I'm attempting to run v0.2.0 of Clair3-rna and have some observations:
```
docker run -v `pwd`:/data -it hkubal/clair3-rna:v0.2.0 /opt/bin/run_clair3_rna --bam_fn /data/test.bam --re…