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10XGenomics / cellranger

10x Genomics Single Cell Analysis
https://www.10xgenomics.com/support/software/cell-ranger
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cellranger vdj defined less cells, than expected #80

Closed soda-bottle closed 10 months ago

soda-bottle commented 4 years ago

Hi! I tried to analyze PBMCs of a Healthy Donor (v1) dataset from 10x website, using cellranger vdj. So I've downloaded VDJ Ig - FASTQs and ran the pipeline with this (refdata-cellranger-vdj-GRCh38-alts-ensembl-3.1.0)reference. Compared to summary for this dataset, provided on website, I've got ~10 times less cells and as a consequence 10 times more reads per cell. QC (Q30, number of reads and correct barcodes) is the same for my summary and the one on website. I was wondering, what could be the issue? Thanks in advance!

I ran the pipeline with the following command: cellranger vdj --id=cell_ranger_1_1 \  --fastqs=/home/stasya/pbmc/vdj_v1_hs_pbmc3_b_26x91_fastqs/ \ --sample=vdj_v1_hs_pbmc3_b_26x91 \ --reference=/home/stasya/cell_ranger/refdata-cellranger-vdj-GRCm38-alts-ensembl-3.1.0

felixhell2004 commented 1 year ago

Do you use 'cellranger count ' this functions to call cells, which to identify the the real cells by barcode?