savagedude3 / MintChIP

pipeline for MintChIP

MintChIP

pipeline for MintChIP

install

requirements

nextflow

fastqc

Je

trimmomatic

bwa

samtools

Homer

R, ChIPQC[http://bioconductor.org/packages/release/bioc/html/ChIPQC.html]

install

git clone https://github.com/jianhong/MintChIP.git

configuration

edit the nextflow.config file depend on your local setting.

prepare barcode file

barcode file should be a text file with two columns: sample_Name and barcode. sample file is bar.txt

prepare fastq files

put the original fastq files in the folder of ${dataDir}/fastq/original/

prepare inputs

put the inputs for the samples with inputs. sample file is inputs.txt. The column should be treatment fastq file name, treatment barcode file name, input fastq file name, input barcode file name.

prepare additional parameters

put additional parameters for findPeaks or trimmomatic in a text file. sample file is findPeaks.txt. The delimiter must be tab.

run pipeline

nextflow run main.nf --dataDir fastq/original --barcode bar.txt

with inputs

nextflow run main.nf --dataDir fastq/original --barcode bar.txt --inputs inputs.txt

with additional parameters for findPeaks

nextflow run main.nf --dataDir fastq/original --barcode bar.txt --findPeaks findPeaks.txt

with additional parameters for trimmomatic

nextflow run main.nf --dataDir fastq/original --barcode bar.txt --trim trimmomatic.txt

output

The output files will be in the folder of results be default. You can change it in the nextflow.config file.