The number of cells is not consistent with the result of cellranger

[Yuanqingq]

Hello! When I use scTE, I have some questions about the number of cells of the results.

I ran cellranger as the code below: cellranger count --id ${sample} --sample ${sample} --transcriptome ~/dm6_cellranger --fastqs ./ --localcores 20

and I ran scTE as the code: scTE -i ${sample}/outs/possorted_genome_bam.bam -o ${sample} -x ~/dm6.exclusive.idx --hdf5 True -CB CB -UMI UB -p 24

When I analysed the results with Seurat, I found cellcounts of the two results are not consistent.

Convert("sample.h5ad", dest = "h5seurat", overwrite = TRUE) Warning: Unknown file type: h5ad Warning: 'assay' not set, setting to 'RNA' Creating h5Seurat file for version 3.1.5.9900 Adding X as data Adding X as counts Adding meta.features from var Seurat.obj <- LoadH5Seurat("sample.h5seurat") Validating h5Seurat file Warning: Feature names cannot have underscores ('_'), replacing with dashes ('-') Initializing RNA with data Adding counts for RNA Adding feature-level metadata for RNA Adding command information Adding cell-level metadata Adding miscellaneous information Adding tool-specific results Seurat.obj An object of class Seurat 3113 features across 1545 samples within 1 assay Active assay: RNA (3113 features, 0 variable features) 2 layers present: counts, data

obj <- Read10X(data.dir = "sample/") Seurat.obj2 <- CreateSeuratObject(counts = obj, project = "sample", min.cells = 3, min.features = 200) Seurat.obj2 An object of class Seurat 12338 features across 7958 samples within 1 assay Active assay: RNA (12338 features, 0 variable features) 1 layer present: counts

As the results show, scTE result has 1545 cells but the cellranger result has 7958 cells. I wonder whether I have made anything wrong, thus resulting the difference.

Many thanks!

Yuanqingq

[BitterWood]

scTE has the option as min_genes and min_counts. Use scTE -h to see them.