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安装CellRanger
https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest?
cd ~/APP
wget -O cellranger-7.1.0.tar.xz "https://cf.10xgenomics.com/releases/cell-exp/cellranger-7.1.0.tar.xz?Expires=1674686023&Policy=eyJTdGF0ZW1lbnQiOlt7IlJlc291cmNlIjoiaHR0cHM6Ly9jZi4xMHhnZW5vbWljcy5jb20vcmVsZWFzZXMvY2VsbC1leHAvY2VsbHJhbmdlci03LjEuMC50YXIueHoiLCJDb25kaXRpb24iOnsiRGF0ZUxlc3NUaGFuIjp7IkFXUzpFcG9jaFRpbWUiOjE2NzQ2ODYwMjN9fX1dfQ__&Signature=kBEWDvHNogaTb-bmHzd7kHIBIfs8LQmePXusMXNKYpuqbgNHX5Ai0mhB-wv6ig1X5QFZytrl4gYXd8DyNXVo85hRp6Iw9k1UHtuuictpnyNe-5JNocePNKou89k9AOEGoatr6xa9z1VPkOj33FTpG25OpfQowpBrwvNhFF27qoSqw7EcjSWm53zB4QsYqMR~Bi-5MXTEplAxusXnE5A1HtVOo31lsL7cavd88ez9yFcSDIf65~KJR6KqDzqYS3NAcm3MKBWWSeIVAwOWAuHaQONeAew8X4fMb3ql85CpeaCWrQdB-vlUVkQbM0gJY2S7MQ9SJ0B5qUc7qo9UWLXATw__&Key-Pair-Id=APKAI7S6A5RYOXBWRPDA"
tar -xf cellranger-7.1.0.tar.xz
ln -s ~/APP/cellranger-7.1.0/bin/cellranger ~/APP/bin/cellranger
export PATH=$HOME/APP/bin:$PATH
index
10X提供人和鼠的基因组参考index,其他物种可以是用cellranger自行构建
# Human reference (GRCh38) md5sum: dfd654de39bff23917471e7fcc7a00cd
wget https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-GRCh38-2020-A.tar.gz
md5sum refdata-gex-GRCh38-2020-A.tar.gz
tar -xf refdata-gex-GRCh38-2020-A.tar.gz
下载原始数据
CNCB的原始数据需要申请,申请通过后可以下载meta data
https://ngdc.cncb.ac.cn/gsa-human/browse/HRA000728