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fastq文件

index

read1

read2

cellraner count 之后

taotao 

#p10  ##因为是bam转fastq得到的，且前缀都是bamtofastq
cd /seu_share/home/chaojie/230218989/taotao/scRNA_seq/03_cellranger_counts
ref=/seu_share/home/chaojie/230218989/datasets/cellranger_ref_data/hg19
id=p10
fastqs=/seu_share/home/chaojie/230218989/taotao/scRNA_seq/02raw_fastq/P10_cSCC_scRNA.bam.1/T23-HTVGLBBXX_MissingLibrary_1_HTVGLBBXX

cellranger count --id=$id \
--transcriptome=$ref \
--fastqs=$fastqs \
--sample=bamtofastq \
--nosecondary
 

noredundancy 

 olp

cd /seu_share/home/chaojie/230218989/20240120_olp/03_cellranger_counts

BASE_DIR="/seu_share/home/chaojie/230218989/20240120_olp/01_rawdata" # 修改为你的父目录路径
REF="/seu_share/home/chaojie/230218989/datasets/cellranger_ref_data/human_hg38/refdata-gex-GRCh38-2020-A" # 基因组参考路径

# 遍历每个样本文件夹
for SAMPLE_DIR in $BASE_DIR/*; do
    if [ -d "$SAMPLE_DIR" ]; then
        SAMPLE_NAME=$(basename "$SAMPLE_DIR")
        FASTQ_PATHS=""

        # 遍历样本中的每个子文件夹，并收集路径
        for SUB_DIR in "$SAMPLE_DIR"/*; do
            if [ -d "$SUB_DIR" ]; then
                FASTQ_PATHS="${FASTQ_PATHS}${SUB_DIR},"
            fi
        done

        # 移除路径列表末尾的逗号
        FASTQ_PATHS=${FASTQ_PATHS%?}

        # 构建并运行 cellranger count 命令
        if [ ! -z "$FASTQ_PATHS" ]; then
            echo "Running cellranger count for $SAMPLE_NAME with FASTQs from $FASTQ_PATHS"
            echo " "
            echo"这是我的运行命令： /seu_share/home/chaojie/230218989/software/cellranger-6.1.2/bin/cellranger count --id=$SAMPLE_NAME \
            --transcriptome=$REF \
            --fastqs=$FASTQ_PATHS"
            echo "\n"
            echo " "
            echo " "
            
            /seu_share/home/chaojie/230218989/software/cellranger-6.1.2/bin/cellranger count --id=$SAMPLE_NAME \
            --transcriptome=$REF \
            --fastqs=$FASTQ_PATHS
        fi
    fi
done