安装¶
要求
- 32G内存或者更高 (根据参考基因组大小确定)
- Linux
- conda环境管理器
使用conda安装
创建环境
conda create -n scope
激活环境
conda activate scope
安装scopetools
conda install -c singleronbio scope-tools
验证安装完成
scope -h Usage: scope [OPTIONS] COMMAND1 [ARGS]... [COMMAND2 [ARGS]...]... Single Cell Omics Preparation Entity Tools Options: --version Show the version and exit. -h, --help Show this message and exit. Commands: STAR STAR short help barcode extract barcode and umi short help cluster cluster short help count count short help cutadapt cutadapt short help featureCounts featureCounts short help run run short help
准备参照基因组
Homo sapiens
wget ftp://ftp.ensembl.org/pub/release-99/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz wget ftp://ftp.ensembl.org/pub/release-99/gtf/homo_sapiens/Homo_sapiens.GRCh38.99.gtf.gz mkdir -p references/Homo_sapiens/Ensembl/GRCh38 gzip -c -d Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz > references/Homo_sapiens/Ensembl/GRCh38/Homo_sapiens.GRCh38.fa gzip -c -d Homo_sapiens.GRCh38.99.gtf.gz > references/Homo_sapiens/Ensembl/GRCh38/Homo_sapiens.GRCh38.99.gtf conda activate scope gtfToGenePred -genePredExt -geneNameAsName2 references/Homo_sapiens/Ensembl/GRCh38/Homo_sapiens.GRCh38.99.gtf /dev/stdout | \ awk '{print $12"\t"$1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10}' > references/Homo_sapiens/Ensembl/GRCh38/Homo_sapiens.GRCh38.99.refFlat STAR \ --runMode genomeGenerate \ --runThreadN 6 \ --genomeDir references/Homo_sapiens/Ensembl/GRCh38 \ --genomeFastaFiles references/Homo_sapiens/Ensembl/GRCh38/Homo_sapiens.GRCh38.fa \ --sjdbGTFfile references/Homo_sapiens/Ensembl/GRCh38/Homo_sapiens.GRCh38.99.gtf \ --sjdbOverhang 100
Mus musculus
wget ftp://ftp.ensembl.org/pub/release-99/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz wget ftp://ftp.ensembl.org/pub/release-99/gtf/mus_musculus/Mus_musculus.GRCm38.99.gtf.gz mkdir -p references/Mus_musculus/Ensembl/GRCm38 gzip -c -d Mus_musculus.GRCm38.dna.primary_assembly.fa.gz > references/Mus_musculus/Ensembl/GRCm38/Mus_musculus.GRCm38.fa gzip -c -d Mus_musculus.GRCm38.99.gtf.gz > references/Mus_musculus/Ensembl/GRCm38/Mus_musculus.GRCm38.99.gtf conda activate scope gtfToGenePred -genePredExt -geneNameAsName2 references/Mus_musculus/Ensembl/GRCm38/Mus_musculus.GRCm38.99.gtf /dev/stdout | \ awk '{print $12"\t"$1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10}' > references/Mus_musculus/Ensembl/GRCm38/Mus_musculus.GRCm38.99.refFlat STAR \ --runMode genomeGenerate \ --runThreadN 6 \ --genomeDir references/Mus_musculus/Ensembl/GRCm38 \ --genomeFastaFiles references/Mus_musculus/Ensembl/GRCm38/Mus_musculus.GRCm38.fa \ --sjdbGTFfile references/Mus_musculus/Ensembl/GRCm38/Mus_musculus.GRCm38.99.gtf \ --sjdbOverhang 100