cellranger count error - Githubissues

我用prefetch下载了SRR9313023的sra文件，接着用fast-dump --split-files --gzip分成了两个fastq文件，之后我将两个文件重命名为R1、R2进行cellranger count。结果报错：

I downloaded the sra file of SRR9313023 with prefetch, and divided it into two fastq files with fast dump -- split files -- gzip. Then I renamed the two files R1 and R2 for cell Ranger count. I got the error:

An extremely low rate of correct barcodes was observed for all the candidate chemistry choices for the input: Sample SRR9313023 in "/XXX/Documents/data/SCell/SSc/GSE132869/fastq". Please check your input data.
- 0.2% for chemistry SC3Pv3
- 0.2% for chemistry SC3Pv3HT
- 0.0% for chemistry SC5P-R2
- 0.0% for chemistry SC3Pv2
- 0.0% for chemistry SC3Pv3LT

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详细代码：

Detailed code:

#step1
prefetch SRR9313023 --max-size 20G
#step2
fastq-dump --split-files --gzip --outdir ./fastq SRR9313023
#step3
cd fastq
mv SRR9313023_1.fastq.gz SRR9313023_S1_L001_R1_001.fastq.gz
mv SRR9313023_2.fastq.gz SRR9313023_S1_L001_R2_001.fastq.gz
cd ..
cellranger count --id=SRR9313023_out \
                 --transcriptome=/XXX/Documents/gtf/refdata-gex-mm10-2020-A \
                 --fastqs=/XXX/Documents/data/SCell/SSc/GSE132869/fastq \
                 --sample=SRR9313023

10XGenomics / cellranger

cellranger count error #158