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Hello,
I used the following commond generating the genes/TEs expression matrix and imported into scanpy to cluster, visualization.
But, the gene expression generated from scTE were largely not con…
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Hi,
I used the 'cellranger multi' command (cellranger v6.1.1) to process my data. I am now trying to use velocyty (v0.17.17) to ascertain the counts. Is there any guidance on how to use the velocyt…
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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,
I have 2 10X Genomics datasets (BCR and GEX). What are the appropriate parameters setting for TRUST4?
I'm using
f"run-trust4 -1 {f1} -2 {f2} --barcode {f1} --UMI {f1} --readFormat bc:0:15,…
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I ran STARsolo like the code below on google colab pro with a human kidney transplant rejection biopsy sample scrnaseq by 10X 5' chromium v3.1
The output I got was a 700mb bam file and barcodes.tsv, …
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Hi all,
Very new to terra and cellranger, so I will try to provide as much information as possible.
I am trying to run Cellranger count on some data that I have using the terra workflow. Using…
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Hi, just came across digestiflow and it seems like an awesome solution for smaller sequencing groups! I am thinking of implementing it in my organization but for one thing - we are starting to process…
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Hi,
I am having trouble in import cell ranger 3 data in Monocle3. Earlier cell ranger 2 was working fine with Monocle2 library. load_cellranger_data is not working. Error: object 'load_cellranger_mat…
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Hi,
I wonder how the `cellranger_pbmc_3k.csv ` was generated in your instruction? It does not seem to be included in the subdirectory of CellRanger pipeline (v3.1.0/ v4.0.0)? What does "Weight" mean…
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I think the 2 components for BT364 are duplicates. This is after importing the cellranger data from the link in the README.md.
```
> allr[12:13]
$`filtered/BT364_1of2.filtered_gene_matrices`
clas…