Metadata-Version: 2.1
Name: celescope
Version: 1.1.8b0
Summary: GEXSCOPE Single cell analysis
Home-page: https://github.com/zhouyiqi91/CeleScope
Author: zhouyiqi
Author-email: zhouyiqi@singleronbio.com
License: UNKNOWN
Description: 
        # CeleScope
        GEXSCOPE Single Cell Analysis Pipelines  
        [中文文档](https://github.com/zhouyiqi91/CeleScope/wiki)
        
        ## Requirements
        
        - conda
        - git
        - minimum 32GB RAM(to run STAR aligner)
        
        ## Installation
        
        
        1. Clone repo
        `git clone https://github.com/singleron-RD/CeleScope.git`
        
        2. Install conda packages
        ```
        cd CeleScope
        conda create -n celescope
        conda activate celescope
        conda install --file conda_pkgs.txt --channel conda-forge --channel bioconda --channel r --channel imperial-college-research-computing
        ```
        
        3. Install celescope
        ```
        pip install celescope
        # if you are in china, you can use pypi mirror to accelerate downloading
        pip install -i https://pypi.tuna.tsinghua.edu.cn/simple celescope
        ```
        
        4. Install Beta version(optional)
        ```
        # if you want to use Beta version of celescope
        python setup.py install
        ```
        
        ## Reference genome 
        
        ### 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 celescope
        
        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 celescope
        
        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
        ```
        
        ## Usage
        
        ### Single cell RNA-Seq
        
        ```
        conda activate celescope
        celescope rna run\
         --fq1 ./data/R2005212_L1_1.fq.gz\
         --fq2 ./data/R2005212_L1_2.fq.gz\
         --genomeDir /SGR/references/Homo_sapiens/Ensembl/GRCh38\
         --sample R2005212\
         --chemistry auto\
         --thread 4\
        ```
        
        `--fq1` Required. Gzipped FASTQ read 1 file path.
        
        `--fq2` Required. Gzipped FASTQ read 2 file path.
        
        `--genomeDir` Required. Reference genome directory.  
        
        `--sample` Required. Sample name. 
        
        `--chemistry` Chemistry version, default=auto. 
        
        `--thread` Number of threads to use, default=1.
        
        ### Single Cell VDJ
        
        ```
        conda activate celescope
        celescope vdj run\   
         --fq1 {vdj fq1.gz}\
         --fq2 {vdj fq2.gz}\
         --type {TCR or BCR}\
         --sample {sample name}\
         --chemistry auto\
         --thread {thread}\
         --match_dir {match_dir}\
        ```  
        
        `--fq1` Required. Gzipped FASTQ read 1 file path.
        
        `--fq2` Required. Gzipped FASTQ read 2 file path.
        
        `--type` Required. TCR or BCR.   
        
        `--sample` Required. Sample name. 
        
        `--chemistry` Chemistry version, default=auto. 
        
        `--thread` Number of threads to use, default=1.
        
        `--match_dir` Optional. Matched scRNA-Seq directory after running CeleScope.  
        
        
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.6
Description-Content-Type: text/markdown
