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Hi, I am just wondering if there is a recommended QC steps that is recommended for input bams?
For e.g. recommended MAPQ threshold for minimap, removing supplementary reads, etc. ?
Thanks,
Sowm…
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Dear creators of nf-gwas-pipeline,
First a praise: I was looking for such a long time for a nice and well documented GWAS pipeline. I must say I've tried quite a few and there was always an issue so…
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# Planned programming tasks
|Issue|Purpose of change|Task size|Assignee|Status|
|---|---|---|---|---|
|#39|Correct essential user-visible behavior.|1 week||☐|
|#42|Improve library maintainabilit…
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Hello, everyone.
The **Introduction to RNA-seq** is currently empty, so I would like to contribute to it.
As far as I understood it, this episode should contain instructions on how to go from r…
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Hey There,
Thank you for providing a super cool pipeline.
I managed to get it to work with the recent genomad integration, but I got an error at one of the last steps of the pipeline.
My command…
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I now have a spatial transcriptome sequencing bam file with a file size of 58g. As well as VCF files of individual variations in fetuses, Souforce is now used to distinguish cells from maternal and fe…
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Great pipeline!
At least for my samples, freyja deboot takes ages to run. It takes so long that it was running into 16 hour time limits, so I had to modify the configs to let it run longer. Even t…
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this is
this is the error code when reaching the multifastq, this is the same pipeline as #1021
I removed some entries to make it readable.
take note the version of my snakePipes
```bash
$snak…
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The `qc` subcommand requires an 'auxiliary' folder to exist to work. This folder is intended to be provided by `train`. However, chrombpnet will not allow for this folder to exist due to the usage of …
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(Python & GitHub novice here, apologies in advance.)
Running through a tutorial using the 10xGenomics 3K PBMC dataset in Jupyter Notebook on Windows 10, caught an error at sc.pp.calculate_qc_metr…