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### Description of the bug
sample.csv:
```
sample,fastq_1,fastq_2,feature_type
NPC_Astro_Diff_aBeta,NovaSeqX_20240927_LH00181_0041_B22TF5VLT3_bcl-convert_KL_NPC_Astro_Diff_20240916_scRNA_10X_Flex_NP…
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### Name of the tool
cellranger multi
### Tool homepage
https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
### Tool description
is a…
pcm32 updated
2 months ago
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I recently attended HCA Asia, and an attendee requested that Ensembl transcript IDs would be accepted as feature variables for the count matrix, especially for Smart-Seq data. He noted that the reason…
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- [ ] scRNA-seq
- https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_mr#runmkref
- [ ] What about scATAC-seq
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Hi @hxj5 , I have a question regarding 10X 5' scRNA-seq data.
For 5' sequencing, the read containing cell barcode and UMI contains part of the transcript https://kb.10xgenomics.com/hc/en-us/article…
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I have used the raw feature-barcode matrix from https://support.10xgenomics.com/single-cell-gene-expression/datasets/2.1.0/pbmc4k and have ran CellBender with defaults. I am wondering why the test ELB…
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We should make the usage of datasets more heterogenous across the notebooks in the docs.
Practically:
- [ ] select 1, max 3, small datasets (
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```go
if i == 0 || (i > 0 && position_list[i].pos-position_list[i-1].pos > 50000) {
```
https://github.com/10XGenomics/lariat/blob/fca47561ae43f47b0f71f98f7f17598d508af440/go/src/inference/lariat.g…
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[Create synthetic dataset for this paper Integrating spatial gene expression and breast tumour morphology via deep learning](https://www.nature.com/articles/s41551-020-0578-x)
Found from Aquila:
h…
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I am using the code, both from stable and developmental and there is a swift in the plots to the left and down.
this is from the 10xgenomics Secondary analysis pipeline
![A1_10xSecondary Analysis]…