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
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