兰花空转文章：

数据空转GEO数据下载：

wget -c "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE198128&format=file" -O GSE198128_RAW.tar

样本信息

#series_sample_iddevelopmental_stagetissuecodeSRRslide
GSM5939574bud1-6FlowerAM559-ST-010001SRR18292617slide1
GSM5939575bud7FlowerAM559-ST-010003SRR18292616slide2
GSM5939576bud8FlowerAM559-ST-010004SRR18292615slide3

原始fastq数据下载：

#wget -c https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-24/SRR018/18292/SRR18292617/SRR18292617.lite.1
#wget -c https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-zq-38/SRR018/18292/SRR18292616/SRR18292616.lite.1
#wget -c https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-zq-38/SRR018/18292/SRR18292615/SRR18292615.lite.1
#for i in SRR18292615 SRR18292616 SRR18292617;do echo "fasterq-dump --split-3 -O ./ $i.lite.1";echo "pigz $i.lite.1_1.fastq";echo "pigz $i.lite.1_2.fastq";echo "ln -s $i.lite.1_1.fastq.gz ${i}_S1_L001_R1_001.fastq.gz";echo "ln -s $i.lite.1_2.fastq.gz ${i}_S1_L001_R2_001.fastq.gz";done
fasterq-dump --split-3 -O ./ SRR18292615.lite.1
pigz SRR18292615.lite.1_1.fastq
pigz SRR18292615.lite.1_2.fastq
ln -s SRR18292615.lite.1_1.fastq.gz SRR18292615_S1_L001_R1_001.fastq.gz
ln -s SRR18292615.lite.1_2.fastq.gz SRR18292615_S1_L001_R2_001.fastq.gz
fasterq-dump --split-3 -O ./ SRR18292616.lite.1
pigz SRR18292616.lite.1_1.fastq
pigz SRR18292616.lite.1_2.fastq
ln -s SRR18292616.lite.1_1.fastq.gz SRR18292616_S1_L001_R1_001.fastq.gz
ln -s SRR18292616.lite.1_2.fastq.gz SRR18292616_S1_L001_R2_001.fastq.gz
fasterq-dump --split-3 -O ./ SRR18292617.lite.1
pigz SRR18292617.lite.1_1.fastq
pigz SRR18292617.lite.1_2.fastq
ln -s SRR18292617.lite.1_1.fastq.gz SRR18292617_S1_L001_R1_001.fastq.gz
ln -s SRR18292617.lite.1_2.fastq.gz SRR18292617_S1_L001_R2_001.fastq.gz

空转数据分析：

cat $datadir/meta.txt|grep -v "#"|while read series_sample_id developmental_stage  tissue code SRR slide;do 
  
  python3 $scripts/scanpy_st_qc.py \
  -d ../01.spaceranger/$slide/outs/filtered_feature_bc_matrix \
  --image_dir ../01.spaceranger/$slide/outs/spatial/ \
  -p $slide  --library_id $slide -o $slide \
  --metadata_col_name gender age patient  series_sample_id  \
  --metadata_value $series_sample_id $developmental_stage  $tissue $code $SRR $slide \
  --nUMI_min 500  --nGene_min 10 --percent_mito 30 --mito_gene_pattern "^MT-*" 
done



mkdir 02.seurat_data_qc   #创建文件夹
cd 02.seurat_data_qc #进入02.data_qc文件夹


#空间转录组很少过滤 spots，除非是坏死的组织；

cat $datadir/meta.txt|grep -v "#"|while read series_sample_id developmental_stage  tissue code SRR slide;do 
Rscript $scripts/seurat_st_qc.r \
  -d ../01.spaceranger/$slide/outs/filtered_feature_bc_matrix \
  --image_dir ../01.spaceranger/$slide/outs/spatial/ \
  -p $slide  --project LAN --slice $slide  -o $slide \
  --metadata_col_name series_sample_id developmental_stage  tissue code SRR slide \
  --metadata_value $series_sample_id $developmental_stage  $tissue $code $SRR $slide \
  --nUMI_min 500  --nGene_min 10 --percent_mito 30 --mito_gene_pattern "^MT-*" 
done