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Hello,
I am working with a scWGS bam file generated using the cell ranger DNA pipeline, and I would like to use SEACON. Can you please help with the following two issues?
1) Do I need to split …
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## Context
See [**cell-science-modalites**](https://czi-sci.slack.com/archives/C02TSE92DBM/p1713562383176259?thread_ts=1713374968.017459&cid=C02TSE92DBM).
@jahilton writes:
> Solution is to r…
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Hi,
BD Rhapsody now outputs the raw counts in the same format as Cell Ranger V3, in a folder with an .mtx file instead of a .csv.gz file. When I use the pipeline on the .mtx file, it recognises it …
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Hello,
I'm wondering if SoupOrCell can be used with home-brew single-cell data not produced on the 10X Genomics platform and processed through CellRanger? What steps would need to be done (e.g. alter…
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Hi !
I used Cell Ranger pipeline v 4.0.0 for my clustering analysis, and no weight columns were generated in the Cell Ranger file.
Although it says it's backward compatible, I cannot seem to be a…
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Hi!
First of all, thank you for the great tool.
I have single-cell RNA sequencing (cell-ranger) data for e.g 3 donors (=> 3 bam files, one per donor), as well as pooled scRNA-seq data for the sa…
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Hi velocyto team,
I have a quick question regarding the pre-velocyto process using cell ranger. The new Cell Ranger 5.0 has a new "**include-introns**" option for counting intronic reads.
https://…
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**Describe the issue**
I'm making a custom reference (for the chicken genome) and I also want to add the GFP sequence. I have successfully done so following the instructions for cellranger (https://w…
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When I supply Cell Ranger’s `Multiplexing Capture` to `--exclude-feature-types`, the following warning is issued:
```
Specified 'Multiplexing Capture' using --exclude-feature-types, but this is not …
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Hello,
Thank you for this package/website. I tried running a few analysis on my scDNA samples with SCYN and i had no issue.
I'm currently trying to run analysis but directly with the outputs of…