非小细胞肺癌（GSE148071）
非小细胞肺癌（GSE148071）
数据下载：
wget -c "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE148071&format=file" -O GSE148071_RAW.tar
tar xvf GSE148071_RAW.tar
数据map.txt 准备：
GSM4453576 P1 71 female LUSC advanced GSM4453577 P2 62 male LUAD advanced GSM4453578 P3 67 male LUSC advanced GSM4453579 P4 58 male LUSC advanced GSM4453580 P5 62 male LUAD advanced GSM4453581 P6 59 male LUSC advanced GSM4453582 P7 71 male LUSC advanced GSM4453583 P8 35 male LUAD advanced GSM4453584 P9 40 male LUAD advanced GSM4453585 P10 65 male LUSC advanced GSM4453586 P11 58 female NSCLC advanced GSM4453587 P12 62 female LUAD advanced GSM4453588 P13 50 female LUAD advanced GSM4453589 P14 60 male LUSC advanced GSM4453590 P15 64 male LUSC advanced GSM4453591 P16 49 male LUAD advanced GSM4453592 P17 71 male LUSC advanced GSM4453593 P18 66 male LUSC advanced GSM4453594 P19 55 male LUSC advanced GSM4453595 P20 59 male LUAD advanced GSM4453596 P21 65 male LUAD advanced GSM4453597 P22 67 male LUSC advanced GSM4453598 P23 77 male LUSC advanced GSM4453599 P24 52 male LUAD advanced GSM4453600 P25 75 male LUSC advanced GSM4453601 P26 53 female LUSC advanced GSM4453602 P27 68 male LUSC advanced GSM4453603 P28 64 female LUAD advanced GSM4453604 P29 48 male LUAD advanced GSM4453605 P30 73 male LUSC advanced GSM4453606 P31 53 male LUSC advanced GSM4453607 P32 71 female LUAD advanced GSM4453608 P33 42 female LUAD advanced GSM4453609 P34 72 male LUAD advanced GSM4453610 P35 63 male LUAD advanced GSM4453611 P36 42 male LUSC advanced GSM4453612 P37 73 female LUSC advanced GSM4453613 P38 55 male LUAD advanced GSM4453614 P39 49 male LUAD advanced GSM4453615 P40 62 male LUSC advanced GSM4453616 P41 60 male LUSC advanced GSM4453617 P42 64 male NSCLC advanced
数据读入分析：
cat map.txt |while read s t;do
Rscript $scripts/seurat_sc_qc.r --count ${s}_${t}_exp.txt.gz --project GSE148071 \
--metadata.col.name project Capture.Method Sample Tissue\
--metadata.value $project 10X3 $t $s\
--nUMI.min 500 \
--nUMI.max 40000 \
--nGene.min 250 \
--mito.gene.pattern "^MT.*-" \
--percent_mito 20 \
--log10GenesPerUMI 0.7 \
-o $project/ -p $t
done
#合并数据
Rscript $scripts/merge_seurat_obj.r -i `ls *.afterQC.rds` \
-o $project/01.qc -p lung
单细胞课程推荐：
单细胞转录组分析课程推荐：https://bdtcd.xetslk.com/s/4i88K6
- 发表于 2024-08-16 15:10
- 阅读 ( 226 )
- 分类：转录组
