10X Visium 空间转录组分析–上游spaceranger分析

测试开头

首先下载软件：

wget -O spaceranger-1.3.1.tar.gz "https://cf.10xgenomics.com/releases/spatial-exp/spaceranger-1.3.1.tar.gz?Expires=1656124515&Policy=eyJTdGF0ZW1lbnQiOlt7IlJlc291cmNlIjoiaHR0cHM6Ly9jZi4xMHhnZW5vbWljcy5jb20vcmVsZWFzZXMvc3BhdGlhbC1leHAvc3BhY2VyYW5nZXItMS4zLjEudGFyLmd6IiwiQ29uZGl0aW9uIjp7IkRhdGVMZXNzVGhhbiI6eyJBV1M6RXBvY2hUaW1lIjoxNjU2MTI0NTE1fX19XX0_&Signature=mjCOWsva2SuHUyHdwxyx41f~rB9I9XkkIlpk2CHs~am6B9kMdVFhD-EEbZjADZc~uaFtyW79p3AXUSE3~Tm-35xwPUjLpv4pU3BIbNd4DBUYepgS0S3RtyjrjuCxwADxdDPekyBT64q2m9siMG-JfZ~OiKqEcBMlWaBnf822MTrX1ban1rvC~cT1yNPMl7-9cdC13kBx6JpV11qOzY~iF3cIdF6zrHyNkNrmaMG~9jvxbSRVDftoP2nFPjyrksOAQDET5Ga9RI~LRjMHMsglfGX6hesiJo1kWpcWHx1dhK~p7XanhuDJ-tzT-Pn5B9QJsXkCE0QCNHplykUrijdPBg__&Key-Pair-Id=APKAI7S6A5RYOXBWRPDA"

10X Visium 空间转录组分析--上游spaceranger分析

然后安装软件，并尝试能否运行：

tar -xzvf spaceranger-1.3.1.tar.gzexport PATH=/data/yudonglin/software/spaceranger-1.3.1:$PATHspaceranger testrun --id=tiny

10X Visium 空间转录组分析--上游spaceranger分析

然后下载数据开始实战：

mkdir datasets# Download FASTQ to datasets folderwget -c https://s3-us-west-2.amazonaws.com/10x.files/samples/spatial-exp/1.1.0/V1_Adult_Mouse_Brain/V1_Adult_Mouse_Brain_fastqs.tar # Download image file to datasets folderwget -c https://cf.10xgenomics.com/samples/spatial-exp/1.1.0/V1_Adult_Mouse_Brain/V1_Adult_Mouse_Brain_image.tif

10X Visium 空间转录组分析--上游spaceranger分析

管理员权限清除缓存：

echo 1 > /proc/sys/vm/drop_caches

10X Visium 空间转录组分析--上游spaceranger分析

解压数据：

# Extract sample FASTQ filestar -xvf datasets/V1_Adult_Mouse_Brain_fastqs.tar -C datasets/ && rm datasets/V1_Adult_Mouse_Brain_fastqs.tar

10X Visium 空间转录组分析--上游spaceranger分析

开始运行正式的代码：

spaceranger count --id="V1_Adult_Mouse_Brain"                    --description="Adult Mouse Brain (Coronal)"                    --transcriptome=/data/yudonglin/velocity/refdata-gex-mm10-2020-A                    --fastqs=V1_Adult_Mouse_Brain_fastqs                    --image=V1_Adult_Mouse_Brain_image.tif                    --slide=V19L01-041                    --area=C1                    --localcores=40                    --localmem=128
spaceranger count --id="V1_Adult_Mouse_Brain"                   --description="Adult Mouse Brain (Coronal)"                   --transcriptome=/data/yudonglin/velocity/refdata-gex-mm10-2020-A                   --fastqs=datasets/V1_Adult_Mouse_Brain_fastqs                   --image=datasets/V1_Adult_Mouse_Brain_image.tif                   --slide=V19L01-041                   --slidefile=V19L01-041.gpr                   --area=C1                   --localcores=16                   --localmem=128