数据下载与整理：

wget -c https://ftp.ncbi.nlm.nih.gov/geo/series/GSE139nnn/GSE139555/suppl/GSE139555%5Fall%5Fmetadata.txt.gz
wget -c "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE139555&format=file" -O GSE139555_RAW.tar
tar xvf GSE139555_RAW.tar
cat map.txt|while read g s p;do
  mkdir $p
  cd $p
  ln -s ../${g}_$s-$p.matrix.mtx.gz matrix.mtx.gz
  ln -s ../${g}_$s-$p.barcodes.tsv.gz barcodes.tsv.gz
  ln -s ../${g}_$s-$p.genes.tsv.gz features.tsv.gz
  
  cd ..
  
  #逗号换成tab键，并提取相应metadata文件
  zcat GSE139555_all_metadata.txt.gz |sed 's#,#\t#g' |awk 'BEGIN{IGNORECASE=1}NR==1 || $1~"'$p'" '|sed -r 's/^\S+_//'|gzip - >$p.metadata.tsv.gz
done

准备map.txt文件：

GSM4143655	SAM24345862	lt1
GSM4143666	SAM24363329	ln6
GSM4143677	SAM24358050	cn2
GSM4143656	SAM24345863	ln1
GSM4143667	SAM24363331	lb6
GSM4143678	SAM24360638	rt1
GSM4143657	SAM24348188	lt2
GSM4143668	SAM24350754	et1
GSM4143679	SAM24360640	rn1
GSM4143658	SAM24348189	ln2
GSM4143669	SAM24350755	en1
GSM4143680	SAM24360639	rb1
GSM4143659	SAM24349905	lt3
GSM4143670	SAM24350752	et2
GSM4143681	SAM24361563	rt2
GSM4143660	SAM24349906	ln3
GSM4143671	SAM24350753	en2
GSM4143682	SAM24361562	rn2
GSM4143661	SAM24353440	lt4
GSM4143672	SAM24352255	et3
GSM4143683	SAM24361564	rb2
GSM4143662	SAM24353441	ln4
GSM4143673	SAM24352256	en3
GSM4143684	SAM24363036	rt3
GSM4143663	SAM24360809	lt5
GSM4143674	SAM24356595	ct1
GSM4143685	SAM24363037	rn3
GSM4143664	SAM24360810	ln5
GSM4143675	SAM24356596	cn1
GSM4143686	SAM24363038	rb3
GSM4143665	SAM24363330	lt6
GSM4143676	SAM24358049	ct2

数据读入：

project=GSE139555
mkdir $project
cat data/$project/map.txt |while read g s p;do
  Rscript $scripts/seurat_sc_qc.r   --data.dir  $p  --project $project  \
       --metadata.col.name project Capture.Method Sample Tissue\
       --metadata.value $project 10X3 $p NA\
        --nUMI.min 500 \
         --nUMI.max 40000 \
      --nGene.min 250 \
      --mito.gene.pattern "^MT.*-" \
      --percent_mito 20 \
      --log10GenesPerUMI 0.7 \
      -o $project/ -p $p --metadata $p.metadata.tsv.gz
   
done

#合并数据

Rscript $scripts/merge_seurat_obj.r -i `ls $project/*.afterQC.rds` \
    -o $project/01.qc -p lung