下载SRR

点击Send to，选择File，Format选择Accession List，点击Create File，下载自己要下载的SRR号列表

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cat SRR_Acc_List_scATAC.txt |while read id;do (prefetch -X 100G $id &);done #后台下载

参考：
https://zhuanlan.zhihu.com/p/563699865

SRR转fastq

# 单样本
nohup fasterq-dump --split-3 SRR6382584 &           #将双端测序文件拆分为两个reads
# 循环跑多样本
for folder in SRR*; do
    nohup fasterq-dump --split-files -e 20 "$folder" --include-technical -O fastq &
done

参考：
https://www.omicsclass.com/article/1917
https://zhuanlan.zhihu.com/p/563699865

安装cellranger-atac

参考：
https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/installation

重命名fastq

for file in *.fastq; do
    if [[ $file == *"_1.fastq" ]]; then
        mv "$file" "${file/_1.fastq/_S1_L001_I1_001.fastq}"
    elif [[ $file == *"_2.fastq" ]]; then
        mv "$file" "${file/_2.fastq/_S1_L001_R1_001.fastq}"
    elif [[ $file == *"_3.fastq" ]]; then
        mv "$file" "${file/_3.fastq/_S1_L001_R2_001.fastq}"
    elif [[ $file == *"_4.fastq" ]]; then
        mv "$file" "${file/_4.fastq/_S1_L001_R3_001.fastq}"
    fi
done

cellranger-atac count

# 单个样本
cellranger-atac count --id=$sample \
--localcores=40 \
--reference=/home/txm/genome/cellranger_atac/refdata-cellranger-arc-GRCh38-2020-A-2.0.0 \
--fastqs=/home/txm/project/GBM/data/elife_GBM_ATAC/ATAC_raw/fastq/$sample \
--sample=$sample

# 所有样本循环
for sample in sample*; do
 cd /home/txm/project/AD/raw_data/2021_NG_scRNA_scATAC/scATAC/fastq/$sample/
 nohup cellranger-atac count --id=$sample \
    --localcores=10 \
    --reference=/home/txm/genome/cellranger_atac/refdata-cellranger-arc-GRCh38-2020-A-2.0.0 \
    --fastqs=/home/txm/project/AD/raw_data/2021_NG_scRNA_scATAC/scATAC/fastq/$sample/ \
    --sample=$sample \
    --localmem=100 & 
done

参考：
https://zhuanlan.zhihu.com/p/563699865
https://cloud.tencent.com/developer/article/2245873

扩展阅读

https://www.biostars.org/p/9549547/
//www.greatytc.com/p/ab98dd332368
//www.greatytc.com/p/25692cb89505
https://mp.weixin.qq.com/s/efYr4AV_vZeh_ihiZ9Poyg