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I'm attempting to produce Giotto results for the Spatial LIBD data using the [SEDR Analyses](https://github.com/JinmiaoChenLab/SEDR_analyses)
The issue seems to be that the _par_ files are not gett…
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I have the following BAM file, repeat masker GTF and genome GTF.
They are downloadable here:
- [BAM](https://s3-ap-northeast-1.amazonaws.com/stemrim-pub/ewijaya/discuss/velocyto/input.sorted.bam)
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### Project short name: Covid19BALFLandscape
### Primary Wrangler:
Arsenios
### Secondary Wrangler:
Ida
### Associated files
* Google Drive: [folder](https://drive.google.com/drive/folders/1Ua…
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Hi, I’ve got a couple of technical and conceptual questions about using kallisto with the TCC option. For context, I’ve recently read the Commons Cell Atlas paper (https://www.biorxiv.org/content/10.1…
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Hi
I am a python novice and I am interested in using SPRING
With some adaptations I successfully managed to run the pbmc4k tutorial on python 3.7.3
Instead when trying the HPCs tutorial, upon loa…
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Hi,
Thanks for developing this great tool.
I'm running into an error in **LoadH5Seurat()** step, stated that: _Error: Missing required datasets 'levels' and 'values'_.
My data was downloaded …
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**Software versions**
Specify what versions of the following you are using:
- `HTSeq: 0.12.4`
- `Python: 3.8.16`
- Linux
- `pbmm2: 1.13.1`
- `GenomicFeatures: 1.50.4`
**Question**
Dear h…
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Hello,
I am running LinkedSV on a 10x linked-read WGS dataset of a highly rearranged human cell line. The alignment was done previously with the 10x Longranger pipeline. LinkedSV ran through, the r…
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Hi everyone!
Now I am struggling with a couple of issues related to Seurat v5.1.0.
1) I have problems with the subsetting of seurat objects after I create them from matrix, feature and barcode f…
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Hi,
I encountered these two errors while running velocyto... the loom file is created.
2019-02-03 22:25:37,857 - DEBUG - Counting done!
2019-02-03 22:25:38,494 - DEBUG - Example of barcode: AGG…