BatMeth2

BatMeth2

Citation: Zhou Q, Lim J-Q, Sung W-K, Li G: An integrated package for bisulfite DNA methylation data analysis with Indel-sensitive mapping. BMC Bioinformatics 2019, 20:47.

More information is in Github, 中文

I just tried the pipeline but I don’t know exactly how those all work. Maybe I’ll update this later

Install

Requirement

1. gcc (v4.8) , gsl library, zlib
2. R (ggplot2, pheatmap, xtable)
3. samtools (suggest: v1.3.1)
4. fastp, raw reads as input need

## gsl install: sudo apt-get install libgsl0ldbl libgsl0-dev
./configure
make
make copy

Example Data

You can download the test data on here

It contain files:

• input fastq.gz (paired end)
• genome file
• usage code and details
• gene annotation file

BUILDING INDEX

mkdir batmeth2index
cd batmeth2index
BatMeth2 build_index GENOME.fa # WGBS Data set
BatMeth2 build_index rrbs GENOME.fa # RRBS Data set
cd ../

Pipline

---

Quick pipeline

BatMeth2 pipel --aligner=no -1 R1.fq.gz -2 R2.fq.gz -g ./batmeth2index/genome.fa -o meth -p 6 --gff ./gene.gff -f 1

Step by Step

mkdir batmeth2index
cd batmeth2index
BatMeth2 build_index genome.fa # WGBS Data set
cd ../

BatMeth2 align -g ./batmeth2index/genome.fa -i R1.fq.gz -i R2.fq.gz -p 6 -o meth.sam

## Caculate DNA methylation level
BatMeth2 calmeth -g ./batmeth2index/genome.fa -i meth.sam -m meth

## DNA methylation level distribution on gene/TE etc
BatMeth2 annoation -o meth -G ./batmeth2index/genome.fa -gff ./gene.gff -m meth.methratio.txt -B -P --TSS --TTS --GENE

## DNA methylation differential analysis example
BatMeth2 batDMR -g ./batmeth2index/genome.fa -o_dm DM.txt -1 meth_loci.CG.txt -2 mutant_loci.CG.txt -L

Visualization

BatMeth2 methyPlot meth.methBins.txt meth.Methygenome.pdf 0.025 meth.Methylevel.1.txt meth.function.pdf TSS TTS meth.AverMethylevel.1.txt meth.Methenrich.pdf meth.annoDensity.1.txt meth.density.pdf meth meth.mCdensity.txt meth.mCdensity.pdf  meth.mCcatero.txt jcmeth.mCcatero.pdf 0.6 0.1 0.1