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Hello,
I ran cellsnp-lite with the following command for calling variants in mitochondrial transcripts in 10X scRNAseq data and for each of three independent samples, received 16,299 variants, which …
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老师好，我在跑去双细胞过程时遇到了以下报错，这应该是发生在你fix上一个有关的bug后
## devtools::install_github('chris-mcginnis-ucsf/DoubletFinder')
> library("DoubletFinder")#注意一定要先运行
> source("./scRNA_scripts/doubletFinder_v3.R")
> so…
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- [ ] There's still an open ticket to submit updated imaging metadata with channel info: https://sagebionetworks.jira.com/browse/HTAN-557
- [ ] We might also want to update the imaging assay from…
inodb updated
3 weeks ago
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### Description of the bug
I'm having some trouble getting the `test` data to run via `singularity` with `alevin`, specifically if I supply my own genome/annotation. It's failing at `SIMPLEAF_INDEX`
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## Problem Summary
Several values in HuBMAP metadata require consolidation or mapping updates to align with the current standards. The issue affects two categories:
- **Granularity Mismatch Mapp…
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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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Hi,
I am currently trying to combine my processed Visium and scRNAseq data using the multimodal run. Following the tutorial I was able to process the data and was able to see the combine feature (G…
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Hello
Thank you very much for your great work! I run scAllele and got a vcf output. My cells are geneA exon5 knock out cells by CRISPR. But scAllele did not find any deletion in exon5 of geneA.
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### Description of the bug
The `test_full`-profile doesn’t run out-of-the-box on scrnaseq v.2.7.1:
```
nextflow run nf-core/scrnaseq -r 2.7.1 -profile test_full,singularity --outdir results
...
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Cross-posting from https://www.reddit.com/r/bioinformatics/comments/1g6zfu6/simpleaf_index_long_runtime/
Is there some guidance about the expected runtime of `simpleaf index` anywhere?
The post …