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GEO数据下载单细胞原始数据和cellranger分析 #3175

Closed ixxmu closed 1 year ago

ixxmu commented 1 year ago

https://mp.weixin.qq.com/s/eyP4NFWND29AWxTlcJ4tzA

ixxmu commented 1 year ago

GEO数据下载单细胞原始数据和cellranger分析 by 东林的扯淡小屋

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE137665

（确定如何修改文件名）

https://bioinformaticsworkbook.org/dataAnalysis/RNA-Seq/Single_Cell_RNAseq/Chromium_Cell_Ranger.html#gsc.tab=0

https://www.jianshu.com/p/11c4537feb4b

数据链接：https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE137665
       GSM4083916  Cortex Normal SleepGSM4083917  Cortex Sleep DeprivedGSM4083918  Cortex Recovery SleepGSM4083919  Hypothalamus Normal SleepGSM4083920  Hypothalamus Sleep DeprivedGSM4083921  Hypothalamus Recovery SleepGSM4083922  Brainstem Normal SleepGSM4083923  Brainstem Sleep DeprivedGSM4083924  Brainstem Recovery Sleep


#SRX6867695: GSM4083916: Cortex Normal Sleep; Mus musculus; RNA-Seq#https://www.ncbi.nlm.nih.gov/sra?term=SRX6867695
wget -c https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR10139721/SRR10139721 -O SRR10139721.sra#--readTypes=TBB --read1PairFiles=VAL630A1_S7_L001_I1_001.fastq.gz --read2PairFiles=VAL630A1_S7_L001_R1_001.fastq.gz --read3PairFiles=VAL630A1_S7_L001_R2_001.fastq.gz
wget -c https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR10139722/SRR10139722 -O SRR10139722.sra#--readTypes=TBB --read1PairFiles=VAL630A1_S7_L002_I1_001.fastq.gz --read2PairFiles=VAL630A1_S7_L002_R1_001.fastq.gz --read3PairFiles=VAL630A1_S7_L002_R2_001.fastq.gz
wget -c https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR10139723/SRR10139723 -O SRR10139723.sra#--readTypes=TBB --read1PairFiles=VAL630A1_S7_L003_I1_001.fastq.gz --read2PairFiles=VAL630A1_S7_L003_R1_001.fastq.gz --read3PairFiles=VAL630A1_S7_L003_R2_001.fastq.gzcd /data3/yudonglin/jianghongwget -c https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR10139724/SRR10139724 -O SRR10139724.sra#--readTypes=TBB --read1PairFiles=VAL630A1_S7_L004_I1_001.fastq.gz --read2PairFiles=VAL630A1_S7_L004_R1_001.fastq.gz --read3PairFiles=VAL630A1_S7_L004_R2_001.fastq.gz

wget -c https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR10139725/SRR10139725 -O SRR10139725.sra#--readTypes=TBB --read1PairFiles=VAL630A1_S7_L005_I1_001.fastq.gz --read2PairFiles=VAL630A1_S7_L005_R1_001.fastq.gz --read3PairFiles=VAL630A1_S7_L005_R2_001.fastq.gz
wget -c https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR10139726/SRR10139726 -O SRR10139726.sra#--readTypes=TBB --read1PairFiles=VAL630A1_S7_L006_I1_001.fastq.gz --read2PairFiles=VAL630A1_S7_L006_R1_001.fastq.gz --read3PairFiles=VAL630A1_S7_L006_R2_001.fastq.gz

#文件解压fasterq-dump -p --include-technical -S -e 30 -O ./ SRR10139721.srafasterq-dump -p --include-technical -S -e 30 -O ./ SRR10139722.srafasterq-dump -p --include-technical -S -e 30 -O ./ SRR10139723.srafasterq-dump -p --include-technical -S -e 30 -O ./ SRR10139724.srafasterq-dump -p --include-technical -S -e 30 -O ./ SRR10139725.srafasterq-dump -p --include-technical -S -e 30 -O ./ SRR10139726.sra
一个样本名文件夹包含所有该样本的测序数据，单个lane或多个lane，多个样本名文件夹放在同一个文件夹下。如下：是两个lane对同一样本的测序数据，放在同一个以样本名为前缀的文件夹下，R1，R2，R3，I1分别代表read 1，barcode，read 2 和 sample index。这些分别代表什么可以详细的阅读10X ATAC文库构建流程。#https://blog.csdn.net/flashan_shensanceng/article/details/125053156
mv SRR10139721_1.fastq.gz VAL630A1_S7_L001_I1_001.fastq.gzmv SRR10139721_2.fastq.gz VAL630A1_S7_L001_R1_001.fastq.gzmv SRR10139721_3.fastq.gz VAL630A1_S7_L001_R2_001.fastq.gz

mv SRR10139722_1.fastq.gz VAL630A1_S7_L002_I1_001.fastq.gzmv SRR10139722_2.fastq.gz VAL630A1_S7_L002_R1_001.fastq.gzmv SRR10139722_3.fastq.gz VAL630A1_S7_L002_R2_001.fastq.gz

mv SRR10139723_1.fastq.gz VAL630A1_S7_L003_I1_001.fastq.gzmv SRR10139723_2.fastq.gz VAL630A1_S7_L003_R1_001.fastq.gzmv SRR10139723_3.fastq.gz VAL630A1_S7_L003_R2_001.fastq.gz

mv SRR10139724_1.fastq.gz VAL630A1_S7_L004_I1_001.fastq.gzmv SRR10139724_2.fastq.gz VAL630A1_S7_L004_R1_001.fastq.gzmv SRR10139724_3.fastq.gz VAL630A1_S7_L004_R2_001.fastq.gz

mv SRR10139725_1.fastq.gz VAL630A1_S7_L005_I1_001.fastq.gzmv SRR10139725_2.fastq.gz VAL630A1_S7_L005_R1_001.fastq.gzmv SRR10139725_3.fastq.gz VAL630A1_S7_L005_R2_001.fastq.gz

mv SRR10139726_1.fastq.gz VAL630A1_S7_L006_I1_001.fastq.gzmv SRR10139726_2.fastq.gz VAL630A1_S7_L006_R1_001.fastq.gzmv SRR10139726_3.fastq.gz VAL630A1_S7_L006_R2_001.fastq.gz

export PATH=/data/yudonglin/software/cellranger-7.0.0:$PATH#开始运行：cellranger count --id=Cortex_normal \                   --transcriptome=/data/yudonglin/reference/singcell/refdata-gex-mm10-2020-A\                   --fastqs=/data3/yudonglin/jianghong \                   --sample=VAL630A1 \                   --localcores=40 \                   --localmem=64