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Need to add capability for downloading and merging NextSeq files
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Need to clarify what some of the columns in `variants_long_table.csv` file indicate.
There's some inconsistencies sometimes, for example: `REF_DP` + `ALT_DP` doesn't add up; for indels, often `REF_D…
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First weekly progress update of my project (description of my project plan)
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Are there any plans to implement tumour-only calling, perhaps with a panel of normals as Mutect2 does? I have a batch of tumour FFPE samples with no matched normals that I'd quite like to get Strelka …
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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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Hello!
I'm trying to download information from TCGA-UCEC, and I'm having an error with duplicated elements in the columns. When running my query
```
query
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### Contact Details
_No response_
### Description of changes
[workbook (13) (1).xlsx](https://github.com/ranchobiosciences/Data_Modeling_Issues_Templates/files/10795061/workbook.13.1.xlsx)
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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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### Context
A user requested [GSE31704](https://www.refine.bio/experiments/GSE31704).
### Problem or idea
[GSE31704](https://www.refine.bio/experiments/GSE31704) is an Illumina HumanHT-12 V4.…
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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…