msPIPE

Methylation analysis pipeline for WGBS data

Requirements

Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)
Samtools (http://www.htslib.org/)
Bismark (https://github.com/FelixKrueger/Bismark)
cutadapt (https://cutadapt.readthedocs.io/en/stable/)

Or you can use msPIPE on docker without having to prepare the environment.

Download

git clone https://github.com/jkimlab/msPIPE.git

Running

Preparing an input parameter file

The parameter file contains the information necessary for pipeline execution.

### INPUT PARAMETER FILE FORMAT ###

## [DMR]
## ANALYSIS1 = Two sample names for DMR analysis
## ANALYSIS2 = Two sample names for DMR analysis

## [REFERENCE]
## UCSC_NAME = UCSC reference version name
## FASTA = [path to reference fasta file(not required)]
## GTF= [path to reference gtf file(not required)]

## [LIB1]
## SAMPLE_NAME = sample name
## LIB_NAME = library name
## LIB_TYPE = P or S (Paired-End or Single-Read)
## FILE_1 = path to sequencing read file
## FILE_2 = path to sequencing read file

Running pipeline

Running command

/PATH/TO/msPIPE/msPIPE.py -p params.conf -o OUTDIR &> logs

msPIPE options

./msPIPE/msPIPE.py -h

usage: msPIPE.py [-h] --param params.conf --out PATH [--core int]
                 [--qvalue float] [--skip_trimming] [--skip_mapping]
                 [--skip_calling] [--skip_HMR] [--skip_DMR]

optional arguments:
  -h, --help            show this help message and exit
  --param params.conf, -p params.conf
                        config format parameter file
  --out PATH, -o PATH   output directory
  --core int, -c int    core (default:5)
  --qvalue float, -q float
                        q-value cutoff (default:0.5)
  --skip_trimming       skip the trimgalore trimming
  --skip_mapping        skip the bismark mapping
  --skip_calling        skip the methylation calling
  --skip_HMR            skip the HMR analysis
  --skip_DMR            skip the DMR analysis

Running example

Running example using mouse rod WGBS data from Corso-Díaz, Ximena et al.
GEO accession : GSE134873
Used samples
- 24M rep1, rep2, rep3
- 3M rep1, rep2, rep3

params_mouse.conf
Replace the '/PATH/TO/DATA' with a data path on your local server.

[DMR]
ANALYSIS1 = 24M, 3M

[REFERENCE]
UCSC_NAME = mm10

[LIB1]
SAMPLE_NAME = 24M
LIB_NAME = 24M_rep1
LIB_TYPE = P
FILE_1 = /PATH/TO/DATA/SRX6589858_1.fastq.gz
FILE_2 = /PATH/TO/DATA/SRX6589858_2.fastq.gz

[LIB2]
SAMPLE_NAME = 24M
LIB_NAME = 24M_rep2
LIB_TYPE = P
FILE_1 = /PATH/TO/DATA/SRX6589859_1.fastq.gz
FILE_2 = /PATH/TO/DATA/SRX6589859_2.fastq.gz

[LIB3]
SAMPLE_NAME = 24M
LIB_NAME = 24M_rep3
LIB_TYPE = P
FILE_1 = /PATH/TO/DATA/SRX6589860_1.fastq.gz
FILE_2 = /PATH/TO/DATA/SRX6589860_2.fastq.gz

[LIB4]
SAMPLE_NAME = 3M
LIB_NAME = 3M_rep1
LIB_TYPE = P
FILE_1 = /PATH/TO/DATA/SRX6589850_1.fastq.gz
FILE_2 = /PATH/TO/DATA/SRX6589850_2.fastq.gz

[LIB5]
SAMPLE_NAME = 3M
LIB_NAME = 3M_rep2
LIB_TYPE = P
FILE_1 = /PATH/TO/DATA/SRX6589851_1.fastq.gz
FILE_2 = /PATH/TO/DATA/SRX6589851_2.fastq.gz

[LIB6]
SAMPLE_NAME = 3M
LIB_NAME = 3M_rep3
LIB_TYPE = P
FILE_1 = /PATH/TO/DATA/SRX6589852_1.fastq.gz
FILE_2 = /PATH/TO/DATA/SRX6589852_2.fastq.gz

Running command

 ./msPIPE/msPIPE.py -p params_mouse.conf -o mouse_result -c 5 -q 0.5

Using docker

build msPIPE docker image

git clone https://github.com/jkimlab/msPIPE.git
cd msPIPE
docker build -t jkimlab/mspipe:latest .

or you can pull docker image from the docker hub
```
docker pull jkimlab/mspipe:latest
```

run

#docker run -v [local path]:[docker path] [docker image name] [msPIPE command]

docker run -v /PATH/TO/INPUT/DATA:/msPIPE/data:ro -v /PATH/TO/REUSABLE/REFERENCE:/msPIPE/reference -v /PATH/TO/OUTDIR:/work_dir/ jkimlab/mspipe:latest msPIPE.py -p params.conf -o result

Mount the volumes with '-v' options to deliver input data and receive output results.
- input data dir→ /msPIPE/data
- reusable references dir→ /msPIPE/reference
- output dir→ /work_dir
The parameter file must be written based on the internal path of the docker container and placed within the output dir.
All paths must be expressed as absolute paths.
Replace the '/PATH/TO/*' with a directory path on your local server.

CONTACT

bioinfolabkr@gmail.com

nayoung9/msPIPE