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I ran NanoCaller v3.6.0 on ONT NA24385 data using the default parameters:
`NanoCaller --bam ${bam} --ref ${reference} --cpu 15`
I also tried specifying the SNP and indel models:
`NanoCaller --ba…
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Hi
I am very new to ArchR . I have downloaded a public dataset and i indexed the fastq with hg19 as they mentioned in paper.This created sam file, which i converted into bam and then indexed the bam.…
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Problem described here https://github.com/GMOD/jbrowse-components/issues/4637
Basically, i'm not sure why it is using the `--output-fmt-option no_ref` since it requires a reference just above that …
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Hello Weilong. It's a wonderful tool for methylation downstream analysis.
Because it takes a long time for Bsseeker2 to align my data, I chose bwameth for mapping and was generating bam files. And I …
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Hi,
I am confused about `--phasing-vcf phased.vcf`, I don't know which phased.vcf should I choose.
```
severus --target-bam phased_tumor.bam --control-bam phased_normal.bam --out-dir severus_out …
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When I use macs3 call peak(for atac), I only get 5500 peaks, But when I checked the bio company's report, they got a peak of 30,000.
I want to know the possible reasons。
Here's my code：
macs3 callp…
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This is the line: https://github.com/iobio/bam.iobio/blob/6b6970e32cc670e1e263e05cdf43022588fcb678/index.html#L331
This can be tested by launching bam from https://mosaic-staging.chpc.utah.edu
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PHIẾU GHI NHẬN LỖI PHÁT SINH
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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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-b, --bed BED file with repeat coordinates
-o, --out Output tsv path
--trid TRID of a specific repeat to analyze, should be in the BED file
-@ …