Pipeline.rst

Pipeline

Tip

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

• Alignment
• Calmeth
• MethyGff
• bt2bigwig
• PlotMeth
• DiffMeth

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
Calmeth	BS-seq align sorted sam/bam file	methratio file (loci/region)	Perform DNA methylation visulization on chromosome, and diff analysis
MethyGff	methration file from calmeth	methlevel file on genes/TEs etc.	DNA methylation profile or heatmap on genes/TEs/peak regions/etc.
bt2bigwig	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

2. Build index using for rrbs data

$ BatMeth2 index_rrbs -g genomefile 

Main Alignment paramaters

**[ Fastq Quality Con	reol ]**
--fastp	fastp program location
If --fastp is not def	ined, 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 paramate	rs ]**
-g	Name of the genome mapped against
-i
Name of input fi input files can	le, if paired-end. please use -1, -2, 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 usin default step: 5	g an overlapping sliding window of 100000bp at a step of 50000bp0000(bp)

MethyGff/Annoation paramaters

--gtf/--gff/--bed/--b	ed4/--bed5
gtf / gff / bed bed5: Chr start	files, bed: Chr start end; bed4: Chr start end strand; end id strand;
-d/--distance
DNA methylation The distance of	level distributions in body and <INT>-bp flanking sequences. upstream and downstream. default:2000
--step
Gene body and th of the sequence step: 0.025 (2.5	eir flanking sequences using an overlapping sliding window of 5%length at a step of 2.5% of the sequence length. So default %)
-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.