10X Single Cell: Specifying Input FASTQs error()

使用以下命令时出现的报错:

cellranger count --fastqs=${fastq_dir} \
        --transcriptome=${ref_dir}/Human_index \
        --localcores=30 \
        --sample=file1,file2 \
        --id=disease

报错原因是我的fa文件命名方式为:

file1_1.fastq.gz, file1_2.fastq.gz
file2_1.fastq.gz, file2_2.fastq.gz

但是 cellranger 要求的 fastq 标准命名方式为:

[Sample Name]_S1L00[Lane Number]_[Read Type]_001.fastq.gz
Where Read Type is one of:
I1: Sample index read (optional)
I2: Sample index read (optional)
R1: Read 1
R2: Read 2

[Sample Name]_S1L00[Lane Number]_[Read Type]_001.fastq.gz
Where Read Type is one of:
I1: Sample index read (optional)
I2: Sample index read (optional)
R1: Read 1
R2: Read 2

因此只需要把file1_1.fastq.gz, file1_2.fastq.gz,file2_1.fastq.gz, file2_2.fastq.gz 改为 cellranger 要求的 fastq 标准命名方式即可。

修改以后变为:
file1_S1_L001_R1_001.fastq.gz, file1_S1_L001_R2_001.fastq.gz
file2_S1_L001_R1_001.fastq.gz, file2_S1_L001_R2_001.fastq.gz

重命名后再跑以下脚本就没有问题了

cellranger count --fastqs=${fastq_dir} \
        --transcriptome=${ref_dir}/Human_index \
        --localcores=30 \
        --sample=file1,file2 \
        --id=disease
————————

使用以下命令时出现的报错:

cellranger count --fastqs=${fastq_dir} \
        --transcriptome=${ref_dir}/Human_index \
        --localcores=30 \
        --sample=file1,file2 \
        --id=disease

报错原因是我的fa文件命名方式为:

file1_1.fastq.gz, file1_2.fastq.gz
file2_1.fastq.gz, file2_2.fastq.gz

但是 cellranger 要求的 fastq 标准命名方式为:

[Sample Name]_S1L00[Lane Number]_[Read Type]_001.fastq.gz
Where Read Type is one of:
I1: Sample index read (optional)
I2: Sample index read (optional)
R1: Read 1
R2: Read 2

[Sample Name]_S1L00[Lane Number]_[Read Type]_001.fastq.gz
Where Read Type is one of:
I1: Sample index read (optional)
I2: Sample index read (optional)
R1: Read 1
R2: Read 2

因此只需要把file1_1.fastq.gz, file1_2.fastq.gz,file2_1.fastq.gz, file2_2.fastq.gz 改为 cellranger 要求的 fastq 标准命名方式即可。

修改以后变为:
file1_S1_L001_R1_001.fastq.gz, file1_S1_L001_R2_001.fastq.gz
file2_S1_L001_R1_001.fastq.gz, file2_S1_L001_R2_001.fastq.gz

重命名后再跑以下脚本就没有问题了

cellranger count --fastqs=${fastq_dir} \
        --transcriptome=${ref_dir}/Human_index \
        --localcores=30 \
        --sample=file1,file2 \
        --id=disease