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cellranger count: an extremely low rate of correct barcodes was observed

I am new to cellranger. And I tried to run cellranger count for a fastq.gz file.

My code is something like this: (** is just to replace my address name due to privacy issue)

fastq-dump --outdir fastq --split-files --gzip SRR6334434

wget https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2020-A.tar.gz

gunzip refdata-gex-mm10-2020-A.tar.gz

tar -xvf prefdata-gex-mm10-2020-A.tar 

cellranger count --id 3 --fastqs /home/*******/20230515\ Ido\ Amit\ Cell\ 2015/fastq/ --sample SRR6334435 --transcriptome /home/*******/20230515\ Ido\ Amit\ Cell\ 2015/refdata-gex-mm10-2020-A --localcores=8 --localmem=64

And the output is like this:

[error] Pipestance failed. Error log at: 3/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_CHEMISTRY_DETECTOR/_GEM_WELL_CHEMISTRY_DETECTOR/DETECT_COUNT_CHEMISTRY/fork0/chnk0-u949463768b/_errors

Log message: An extremely low rate of correct barcodes was observed for all the candidate chemistry choices for the input: Sample SRR6334435 in "/home/******/20230515 Ido Amit Cell 2015/fastq". Please check your input data.
- 0.2% for chemistry SC3Pv3
- 0.0% for chemistry SC5P-PE
- 0.0% for chemistry SC3Pv2
- 0.0% for chemistry SC3Pv3LT

I don't know what happens and how to fix it. I think they use illumina NextSeq 500 to do the scRNA seq. Thank you very much if you could help me.

cellranger scrnaseq
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updated by GenoMax GenoMax • written by Alex • Alex

1 answer

SRR6334434 is not 10x data.

It is Agilent Sureselect V11 capture data see the metadata table here: https://trace.ncbi.nlm.nih.gov/Traces/?view=run_browser&acc=SRR6334434&display=metadata

If you are looking for single cell data from this project you can find a complete list of samples here: https://trace.ncbi.nlm.nih.gov/Traces/study/?acc=SRP125899&o=acc_s%3Aa

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written by GenoMax GenoMax

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