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snmC-seq3 and snm3C-seq Mapping Pipeline

Installation

To install mapping packages, we recommend using python package manager mamba (faster) or conda:

All the packages and mapping environment can be created by

# this creates a environment called mapping, containing all packages
mamba env create -f mapping_env.yaml
# activate the enviroment before run mapping
mamba activate mapping

Build genome index

Bismark genome index is built by bismark_genome_preparation using default parameters, see documentation in: https://rawgit.com/FelixKrueger/Bismark/master/Docs/Bismark_User_Guide.html

All genome sequence and related files downloaded from: https://hgdownload.cse.ucsc.edu/goldenpath/mm10/bigZips/

Run mapping

The two FASTQ files for a single cell (downsampled) can be used to test the pipeline.

# run snmC mapping
cd snmC_example/
snakemake -j n_cpu --snakefile ./Snakefile

# run snm3C mapping
cd snm3C_example
snakemake -j n_cpu --snakefile ./Snakefile

Mapping steps for a single cell

snmC

snmc

snm3C

snm3c

Mapping example files:

.
├── mapping_env.yaml  # package information YAML file, can be used by mamba/conda to create mapping environment
├── snm3C_example  # minimum snm3C Bismark mapping pipeline example
│   ├── Snakefile
│   ├── fastq
│   │   ├── CEMBA3C_18A3C_R2_P10-1-O5-A2-R1.fq.gz
│   │   └── CEMBA3C_18A3C_R2_P10-1-O5-A2-R2.fq.gz
│   ├── mm10.main.chrom.sizes
│   └── snm3C_steps.svg  # visualization of snm3C mapping steps
└── snmC_example  # minimum snmC Bismark mapping pipeline example
    ├── Snakefile
    ├── fastq
    │   ├── CEMBA200707_9E_1-1-A18-A1-R1.fq.gz
    │   └── CEMBA200707_9E_1-1-A18-A1-R2.fq.gz
    └── snmC_steps.svg  # visualization of snmC mapping steps