Instructions

Install m6APipe

There are two Installation methods for m6APipe.

Running test

In the directory of m6APipe

Conda

nextflow main.nf -c nextflow.config \
  --readPaths test_data \
  --designfile test_data/designfile_test.csv \
  --comparefile test_data/comparefile.txt \
  -resume

Docker

Before running the command, you need to pull the image ( kingzhuky/m6apipe ) from docker hub.

nextflow main.nf -c nextflow.config -profile docker \
  --readPaths test_data \
  --designfile test_data/designfile_test.csv \
  --comparefile test_data/comparefile.txt \
  -resume

Running your own data

Modify nextflow.config

General parameter

Edit parameters that change infrequently in nextflow.config, just list 'fasta', 'gtf' and the main parameters of analysis mode

  fasta = "/home/zky/m6apipe/Genome/hg38/hg38_genome.fa"
  gtf = "/home/zky/m6apipe/Genome/hg38/hg38_genes.gtf"
  // Setting main parameters of analysis mode 
  aligners = "star"   // "star" OR "bwa" OR "tophat2" OR "hisat2" OR "none"
  peakCalling_mode = "independence" // "group" OR "independence"
  peakMerged_mode = "rank" // "rank" OR "macs2" OR "MATK" OR "metpeak" OR "mspc"
  expression_analysis_mode = "DESeq2" // "DESeq2" OR "edgeR" OR "none"
  methylation_analysis_mode = "QNB" // "MATK" OR "QNB" OR "Wilcox-test" OR "MeTDiff" OR "edgeR" OR "DESeq2"

Option parameter

Setting aligners' index according to aligner you chose( Default: "star" )

  tophat2_index = "/Path/to/Tophat2Index/*"
  hisat2_index = "/Path/to//Hisat2Index/*"
  bwa_index = "/Path/to/BWAIndex/*"
  star_index = "/Path/to/starindex"

Setting designfile and comparefile

Designfile

Edit the nextflow.config and define "readPaths", "aligners", "designfile", "comparefile" and correspondiente alignment index for recommend. Designfile is just like the following table with a comma (,) separated, which is .csv suffix file.

Sample_ID	input_FileName	ip_FileName	Group
H1A_Endo	A	B	group_Endo
H1A_ES	C	D	group_ES
H1B_Endo	E	F	group_Endo
H1B_ES	G	H	group_ES

Tips

1. A, B, C... mean the filenames of data, just like A.fastq.gz.
2. If your data is .fastq.gz suffix file, please add the parameter of gzip, just like "--gzip true".
3. If your filename of data is "Hela_cell_input.fastq.gz", please write its filename as "Hela_cell_input".

Comparefile

Comparefile is just like the following text which is a "_vs_" between two groups.

group_Endo_vs_group_ES

Running command

data: fastq.gz

nextflow /path/to/m6APipe/main.nf -c /path/to/m6APipe/nextflow.config \
  --readPaths /path/to/data/ \
  --designfile /your/designfile.csv \
  --comparefile /your/comparefile \
  --gzip \
  -resume

data: fastq

nextflow /path/to/m6APipe/main.nf -c /path/to/m6APipe/nextflow.config \
  --readPaths /path/to/data/ \
  --designfile /your/designfile.csv \
  --comparefile /your/comparefile \
  --gzip false\
  -resume

data: bam

nextflow /path/to/m6APipe/main.nf -c /path/to/m6APipe/nextflow.config \
  --readPaths /path/to/data/ \
  --designfile /your/designfile.csv \
  --comparefile /your/comparefile \
  --aligners none \
  -resume