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Hi, I am new in bioinformatic field and I am trying to do analysis of RNA seq with zUMIs.
**I wrote the yaml file according the instruction:**
##YAML file- zUMIs.yaml
##########################…
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Use 50G bam file to run DaPars software, the result file contains more than 10,000 genes.
Split the 50G bam file into single cell bam files according to the barcode, and run DaPars software. The DaPa…
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It appears the code base has a hidden dependency on `samtools`. Every run I attempted produced the following error:
`bam has no cell barcodes information, plese make sure the aligner have add the …
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Dear minoda-lab,
Could you please add support for the Singleron GEXSCOPE v2 technology (https://github.com/singleron-RD/CeleScope). The barcode and UMI are build in the following way: C9L16C9L16C9L…
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Hello,
I am relatively new in variant calling using scRNA-Seq. I have 17 datasets from 17 patients. I want to call the variants for each patient. I only need the list of variants in each sample.
Can…
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Hello,
just a few beginner's questions:
(0. I am using a bam file with molecular barcode in XM and cell barcode in XC. This is ok I guess?)
1. How should the barcode file (--bcfile) look like? A …
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from pseudo_bulk import *
adata_RNA,adata_ATAC=find_neighbors(adata_RNA,adata_ATAC)
samplelist=list(set(adata_ATAC.obs['sample'].values)) # sample is generated from cell barcode
tempsample=samplel…
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Hi,
First of all thank you for coming up with such a critical procedure that would effect almost all single cell study.
Background:
We implemented 10x to our in-house method that gives read out…
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I completed the tutorial and two samples of my own without error but now I'm consistently getting this problem with subsequent samples:
```
running souporcell doublet detection
Traceback (most re…
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> Alevin adopts efficient algorithms for cellular-barcode whitelist generation, cellular-barcode correction, lightweight per-cell UMI deduplication and quantification.
Is it possible to use Salmon …