Data preparation

Download sample datasets

Dataset1

• Chemistry: SeekSpace® Single Cell Spatial Transcriptome-seq Kit V1.1 (DDVA)

• Species: Mus musculus

• Tissue: Ovary

• ChipID: 2P241018012A2

sample datasets - md5: 35663411550cfdcd1b99fcd269b66bbc

wget

wget -c -O demo.tar "https://seekgene-public.oss-cn-beijing.aliyuncs.com/software/data/demodata/space/WTHA5.tar"
# decompress
tar xf WTHA5.tar

curl

curl -C - -o demo.tar "https://seekgene-public.oss-cn-beijing.aliyuncs.com/software/data/demodata/space/WTHA5.tar"
# decompress
tar xf WTHA5.tar

Dataset2

• Chemistry: SeekSpace® Single Cell Spatial Transcriptome-seq Kit V1.0 (DDVS)

• Species: Mus musculus

• Tissue: Brain

• ChipID: 2P231224030A4

sample datasets - md5: 208efa2d39d5190abec986e9b25aa685

wget

wget -c -O demo.tar "https://seekgene-public.oss-cn-beijing.aliyuncs.com/software/data/demodata/space/demo.tar"
# decompress
tar xf demo.tar

curl

curl -C - -o demo.tar "https://seekgene-public.oss-cn-beijing.aliyuncs.com/software/data/demodata/space/demo.tar"
# decompress
tar xf demo.tar

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Download and build reference genome

Download-mouse-reference-mm10 - md5: 5d3f8ee65f75f8143ec88f77b1821fd8

wget

wget -c -O mm10.tar.gz "https://seekgene-public.oss-cn-beijing.aliyuncs.com/software/data/reference/mm10.tar.gz"
# decompress
tar -zxvf mm10.tar.gz

curl

curl -C - -o mm10.tar.gz "https://seekgene-public.oss-cn-beijing.aliyuncs.com/software/data/reference/mm10.tar.gz"
# decompress
tar -zxvf mm10.tar.gz

The assembly of the reference genome refers to How to build reference genome?