Pipeline

Tip

BatMeth2 can perform one click analysis or the following modules step by step:

tool

input files

main output file(s)

main application

Alignment

Single/Paired-end fastq/gz files

alignment sam/bam file

Perform DNA methylation level calculation and SNP/ASM detection

Calculate DNA methylation level

BS-seq align sorted sam/bam file

methratio file (loci/region)

Perform DNA methylation visulization on chromosome, and diff analysis

Calulate mC across predefined regions

methration file from calmeth

methlevel file on genes/TEs etc.

DNA methylation profile or heatmap on genes/TEs/peak regions/etc.

Meth2BigWig

methration file from calmeth

bigwig files (c/cg/chg/chh)

Convert DNA methylation file to bigwig format.

PlotMeth

methy files from calmeth/methyGff

methy profile/heatmap/boxplot

visulization of DNA methylation across samples

DiffMeth

methration file from calmeth

Diff methy cytosines/regions

Perform Differential DNA methylation analysis

BatMeth2 pipeline

An easy-to-use, auto-run package for DNA methylation analyses:

Raw reads:

BatMeth2 pipel --fastp ~/location/to/fastp \
-1 Raw_reads_1.fq.gz -2 Raw_read_2.fq.gz \
-g ./batmeth2index/genome.fa \
-o meth -p 8 --gff ./gene.gff

Or clean reads:

BatMeth2 pipel -1 Clean_reads_1.fq.gz -2 Clean_read_2.fq.gz \
-g ./batmeth2index/genome.fa \
-o meth -p 8 --gff ./gene.gff

You can always see all available command-line options via --help:

$ BatMeth2 --help
  • After the program runs successfully, a series of files with '- o' as prefix and DNA methylation level will be generated in the output directory. Please refer to the doc for the specific output file and format details.

  • In addition, there will be an HTML report file containing basic information and statistical results of data analysis.

BatMeth2 pipeline main parameters

Build index

Usage: (must run this step first)

  1. Build index using for wgbs data

$ BatMeth2 index -g genomefile
  1. Build index using for rrbs data

$ BatMeth2 index_rrbs -g genomefile

Main Alignment paramaters

[ Fastq Quality Conreol ]

--fastp

fastp program location

If --fastp is not defined, the input file should be clean data.

[ Main paramaters ]

-o

Name of output file prefix

-O

Output of result file to specified folder, default output to current folder (./)

[ Aligners paramaters ]

-g

Name of the genome mapped against

-i

Name of input file, if paired-end. please use -1, -2, input files can be separated by commas. eg. -1 readA.fq.gz,readB.fq.gz -2 ..

-1

Name of input file left end, if single-end. please use -i

-2

Name of input file left end

-p

Launch <integer> threads

-n

maximum mismatches allowed due to seq. errors [0-1]

Calmeth paramaters

--Qual

calculate the methratio while read QulityScore >= Q. default:20

--redup

REMOVE_DUP, 0 or 1, default 1

--region

Bins for region meth calculate , default 1000bp.

-f

for sam format outfile contain methState. [0 or 1], default: 0 (dont output this file).

--coverage

>= <INT> coverage. default: 4

--binCover

>= <INT> nCs per region. default: 3

--chromstep

>= <INT> nCs per region. default: 3

Chromosome using an overlapping sliding window of 100000bp at a step of 50000bpdefault step: 50000(bp)

MethyGff/Annoation paramaters

--gtf/--gff/--bed/--bed4/--bed5

gtf / gff / bed files, bed: Chr start end; bed4: Chr start end strand; bed5: Chr start end id strand;

-d/--distance

DNA methylation level distributions in body and <INT>-bp flanking sequences. The distance of upstream and downstream. default:2000

--step

Gene body and their flanking sequences using an overlapping sliding window of 5%of the sequence length at a step of 2.5% of the sequence length. So default step: 0.025 (2.5%)

-C

<= <INT> coverage. default:1000

Output files

Output file format and details see "https://github.com/GuoliangLi-HZAU/BatMeth2/blob/master/output_details.pdf".<br>

Output report details see "https://www.dna-asmdb.com/download/batmeth2.html" .<br>

Tip

For feature requests or bug reports please open an issue on github.