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
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
Waiting 6 seconds for UI to do final refresh.
Pipestance failed. Use --noexit option to keep UI running after failure.
不知道哪里出了问题,还望不吝赐教。
详细代码:
#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