Single Cell Analysis Pipelines
Project description
CeleScope
CeleScope is a collection of bioinfomatics analysis pipelines developed at Singleron to process single cell sequencing data generated with Singleron products. These pipelines take paired-end FASTQ files as input and generate output files which can be used for downstream data analysis as well as a summary of QC criteria.
Detailed docs can be found in manual.
Hardware/Software Requirements
- minimum 32GB RAM(to run STAR aligner)
- conda
- git
Installation
- Clone repo
git clone https://gitee.com/singleron-rd/celescope.git
# or
git clone https://github.com/singleron-RD/CeleScope.git
- Install conda packages
cd CeleScope
conda create -n celescope
conda activate celescope
conda install -y --file conda_pkgs.txt --channel conda-forge --channel bioconda --channel r --channel imperial-college-research-computing
- Install celescope
pip install celescope
# Use pypi mirror to accelerate downloading if you are in china
pip install -i https://pypi.mirrors.ustc.edu.cn/simple/ celescope
Reference genome
Homo sapiens
mkdir hs_ensembl_99
cd hs_ensembl_99
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
gunzip Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
gunzip Homo_sapiens.GRCh38.99.gtf.gz
conda activate celescope
celescope rna mkref \
--genome_name Homo_sapiens_ensembl_99 \
--fasta Homo_sapiens.GRCh38.dna.primary_assembly.fa \
--gtf Homo_sapiens.GRCh38.99.gtf
Mus musculus
mkdir mmu_ensembl_99
cd mmu_ensembl_99
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
gunzip Mus_musculus.GRCm38.dna.primary_assembly.fa.gz
gunzip Mus_musculus.GRCm38.99.gtf.gz
conda activate celescope
celescope rna mkref \
--genome_name Mus_musculus_ensembl_99 \
--fasta Mus_musculus.GRCm38.dna.primary_assembly.fa \
--gtf Mus_musculus.GRCm38.99.gtf
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celescope-1.3.2.tar.gz
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