10x的数据可以使用 cellranger mkfastq 产生，下面的例子是两个样本同一个lane测序拆分后分析；第二个例子是同一个样本两个lane测序，需要合并一起分析；

大家注意文件命名方式，蓝色和红色部分；

cellranger命名规则

[Sample Name]_S1_L00[Lane Number]_[Read Type]_001.fastq.gz

# 其中Read Type
# I1: Sample index read (optional)
# R1: Read 1
# R2: Read 2

NCBI下载的数据，为双端reads，不符合cellranger mkfastq出来的命名规则，后续cellranger count 无法读入，因此我们要按上述命名规则重新命名文件：

重新命名：

ln -s DRR450709_1.fastq.gz DRR450709_S1_L001_R1_001.fastq.gz
ln -s DRR450709_2.fastq.gz DRR450709_S1_L001_R2_001.fastq.gz

cellranger命令：

 cellranger count --id=DRR450709 \
   --fastqs=./ \
   --sample=DRR450709 \
   --localcores 20 --create-bam=true \
   --transcriptome=/share/ref/Homo_sapiens/refdata-gex-GRCh38-2024-A/

参考：

https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/mkfastq

python脚本，用于链接 10X测序数据为新文件， 设置命令行参数：

 #链接文件命名规则
 #[Library_Name]_S1_L00[Lane_Number]_[R1/R2]_001.fastq.gz

 # 其中Read Type
 # R1: Read 1
 # R2: Read 2

 有两列表格做为输入，第1列为Run编号，第2列为 Library_Name，如果有相同的Library_Name编号 Lane_Number +1。

Run	Library_Name
SRR27277573	GSM7980884
SRR27277581	GSM7980882
SRR27277619	GSM7980865
SRR27277620	GSM7980864
SRR27277621	GSM7980863
SRR27277622	GSM7980862

 输入文件夹包含如下文件：

SRR27277573_1.fastq.gz SRR27277579_2.fastq.gz SRR27277586_1.fastq.gz SRR27277592_2.fastq.gz SRR27277599_1.fastq.gz SRR27277605_2.fastq.gz SRR27277612_1.fastq.gz SRR27277618_2.fastq.gz SRR27277573_2.fastq.gz SRR27277580_1.fastq.gz SRR27277586_2.fastq.gz SRR27277593_1.fastq.gz SRR27277599_2.fastq.gz SRR27277606_1.fastq.gz SRR27277612_2.fastq.gz SRR27277619_1.fastq.gz

#!/usr/bin/env python3
import os
import argparse
from collections import defaultdict
def create_arg_parser():
    parser = argparse.ArgumentParser(description='Link SRA fastq to 10X library : https://www.omicsclass.com/article/2536')
    parser.add_argument('-i', '--input_dir', default=os.getcwd(), 
                       help='Input directory containing NCBI download fastq files (default: current directory)')
    parser.add_argument('-o', '--output_dir', default=os.getcwd(),
                       help='Output directory for linked files (default: current directory)')
    parser.add_argument('-t', '--table', required=True,
                       help='Tab-delimited table with Run and Library_Name columns')
    parser.add_argument('--force', action='store_true',
                       help='Overwrite existing links/files in output directory')
    return parser
def main():
    parser = create_arg_parser()
    args = parser.parse_args()
    
    # Validate directories
    if not os.path.isdir(args.input_dir):
        raise FileNotFoundError(f"Input directory not found: {args.input_dir}")
    
    os.makedirs(args.output_dir, exist_ok=True)
    
    # Read the table
    run_to_library = {}
    with open(args.table, 'r') as f:
        next(f)  # skip header
        for line in f:
            parts = line.strip().split('\t')
            if len(parts) >= 2:
                run_to_library[parts[0]] = parts[1]
    
    if not run_to_library:
        raise ValueError("No valid entries found in the table file")
    
    # Track lane numbers for each library
    library_lane_counts = defaultdict(int)
    processed_files = 0
    
    # Process each run in the table
    for run, library in run_to_library.items():
        lane_number = library_lane_counts[library] + 1
        library_lane_counts[library] = lane_number
        
        # Process R1 and R2 files
        for read_type in ['1', '2']:
            old_file = os.path.join(args.input_dir, f"{run}_{read_type}.fastq.gz")
            if not os.path.exists(old_file):
                print(f"Warning: Input file not found - {old_file}")
                continue
            
            new_filename = f"{library}_S1_L00{lane_number}_R{read_type}_001.fastq.gz"
            new_file = os.path.join(args.output_dir, new_filename)
            
            # Check if target exists
            if os.path.exists(new_file):
                if args.force:
                    os.remove(new_file)
                else:
                    print(f"Warning: Output file exists (use --force to overwrite) - {new_file}")
                    continue
            
            # Create symbolic link
            try:
                rel_path = os.path.relpath(old_file, args.output_dir)
                os.symlink(rel_path, new_file)
                print(f"Created link: {new_filename} -> {rel_path}")
                processed_files += 1
            except OSError as e:
                print(f"Error creating link {new_file}: {e}")
    
    print(f"\nProcess completed. Successfully created {processed_files} links in {args.output_dir}")
if __name__ == '__main__':
    main()