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I have generated a VCF using BCFtools on CentOS 7. When calling Vartrix, this VCF is not recognized :
Vartrix error. v1.1.14.
Error: failed to open BCF/VCF from /home/ulb/iribhm/atourneu/variant/ATC…
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Hi, I'm trying to run SPLASH on my single cell data, and is it possible to run SPLASH by feeding a bam file with barcode-cell type annotation? I'm currently extracting read names from my bam file and …
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With the "pre-mRNA" GTF, there are no splice junctions, which could cause *alignment* issues in CellRanger's snRNA-seq workflow, as discussed here:
https://github.com/10XGenomics/cellranger/issues/7…
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Hi,
I am running it on a bam file but the error message told me it could be truncated. I am seeking a way how to skip these errors.
Slight data loss is acceptable.
`[W::bam_hdr_read] EOF ma…
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Move to bundles inner entity since the scope of the aggregate is the bundle not the entire project.
Reproduction:
- Aggregate dates included in `projects` inner entity from `projects` endpoint (g…
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I got this error when run spatialCluster:
Error in cluster.FUN(Y = as.matrix(Y), df_j = df_j, nrep = nrep, n = n, :
Mat::init(): requested size is too large; suggest to enable ARMA_64BIT_WORD
h…
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Hi, BAVARIA is a very interesting tool. But I have some confusions when I reproduce results of integrating cells from 10X Genomics and Cusanovich 2018 datasets. I tried to use and fix your code, but i…
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I was going through one of the [papers](https://www.nature.com/articles/s41467-023-40883-w) that uses CellRanger in Plasmodium and it says(See section `Single-cell sequencing and data processing`):
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你好，我现在打算运行这个程序，研究时不太理解输入的文件。
首先是peak_gene_100k_corr.bed这个文件的第三第四列是什么，数据是从哪里来的呢。我使用10X（https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/using/count）做单样本分析时数据其中的一个文件是p…