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**Why?**
* Needed for Surge
**Where do I start?**
* Follow the surge planning template document ([https://docs.google.com/document/d/1tT0VHUGWTo0fGWO5uZ9TFpdwgvpNW400LJLmhV1LGkI/edit](https://docs.…
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Is there an optimized settings/code for Dropseq samples. The tutorials seem to be about other scRNAseq methods and I was wondering if Dropseq would require different settings due to its depth of reads…
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Hey,
Thanks for the great pipeline. I'm having an issue about generating report from cell.counts.rds.
```
processing file: report.Rmd
|.. …
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Hello, this is a amazing tool.
I have some problems when I analysis Dropseq data. Maybe you have some expriences can help me solve these problems
1. After the pipeline of velocyto, I get spliced…
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Hi,
thank you for this great tool.
I am running spacemake for an openST data and encountering the following Error when running `spacemake run --cores 8`:
```Error
KeyError in line 286 of /ho…
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Hello everyone,
I have encountered a violin plot failure which I am unable to resolve. I was able to generate the plot with previous data but suddenly the pipeline gives an error at this process an…
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Hi, I’m just starting out in this field.
We have an scRNA-seq dataset that includes 438 million paired-end reads (2x150bp) from approximately 8000 cells sourced from tissue samples. We processed the …
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Is there anyway that I can specify one PATH to picard? I am on an HPC with an institution and I am assuming that is why I am having this issue. Below is what I have tried and the error that I get from…
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My scope: I want to implement Dropseq for total RNA seq.
Function:
1. TagReadWithGeneFunction
Issue: the gene ID without gene names and transcript were removed. Mostly, those are from miRNA.
R…
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Hi!
Many thanks for all you development efforts!
I have six data sets that I would be interested in benchmarking with Kallisto-bustools, however I just found out that kalllisto bus only suppor…