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In my recent usage of HIBAG, I have hla typed genetic data called from the hg38 reference genome. Though I was able to lifotver the hapmap training data positions, I believe it will be much more accur…
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Dear sir,
We used the Illumina platform to determine the whole genome consensus sequence and to
identify intrahost single nucleotide variants for each patient-derived sample
we want to using DeepS…
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### Is there an existing issue for this?
- [X] I have searched the existing issues
### Description of the Bug/Issue
Hi,
would it be possible to add
errorStrategy 'ignore'
in the VADR process a…
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Hello,
Tb-profiler version v6.2.0 is not reporting "missing positions report" data in the .txt output (default settings). The data is generated in the .json file but in the .txt is transcribed as "…
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Hello,
I have a problem with breakdancer. I try to call structural variants from several bams at the same time but it doesn't work.
First I create the config file :
~/Soft/breakdancer/breakdan…
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Dear all,
I'm studying the germline cells and I isolated single nuclei from single germ cells and sequenced the content with Illumina Hiseq paired-end platform. The Nuclei are huge and gave me enou…
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Last bit of https://github.com/galaxyproject/tools-devteam/issues/92 which was mostly dealt with.
The problem with tophat is that it does not allow arbitrary read groups or at least all of the valid …
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Hello,
I am cleaning some Illumina data, some of them are pretty old, and I get quality of 70 in fastp report.
When I analyze the same file with fastqc, quality score is 40 max and it found the en…
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Hi,
I am using bowtie 2.3.5.1 and try to get sample and other IDs recorded on the `@RG` line. Unfortunately, it seems bowtie2 does not write TABs as separators on the `@RG` line and also copies who…
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Hi there,
I'd like to know why, for some projects (such as TCGA-DLBC), the query returns only "primary tumor" sample types, despite on TCGA it is also present "blood derived normal". I notice that t…