cellranger分析单细胞测序数据

for i in `ls rawdata/Day1/*gz|cut -d '/' -f3 | cut -d '_' -f 1,2,3 |sort |uniq`;

do
        zcat rawdata/Day1/${i}_I1_001.fastq.gz >> mergedata/Day1/Day1_S1_L001_I1_001.fastq
        zcat rawdata/Day1/${i}_R1_001.fastq.gz >> mergedata/Day1/Day1_S1_L001_R1_001.fastq
        zcat rawdata/Day1/${i}_R2_001.fastq.gz >> mergedata/Day1/Day1_S1_L001_R2_001.fastq
done

cellranger count --id=Day1 \
#fastq文件目录
--fastqs=fastq/ \
#注释文件
--transcriptome=cellranger_rn6 \
--sample=Day1 \
--localcores=10