BS-Seq Analysis Pipeline - BatMeth2

BatMeth2 (An Integrated Package for Bisulfite DNA Methylation Data Analysis with Indel-sensitive Mapping.), click here for information on how to use it and source code.

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

In order to complete the DNA methylation data analysis more conveniently, we packaged all the functions to complete an easy-to-use, auto-run package for DNA methylation analysis. During the execution of BatMeth2 Tool, an html report is generated about statistics of the sample.

BatMeth2 pipeline function mode
BatMeth2 Mode Function Details Output
Align BS-seq reads alignment align align results
Calmeth DNA methylation level calculation calmeth calmeth results
Annotation DNA methylation level annotation on gene/te ... annotation annotation results
MethyPlot DNA methylation visualization methyPlot Visualization
MethDM Differential methylation analysis methdm Differential
DM annotation Differential methylation sites annotation dm annotation Differential visual

BS-Seq Pipeline BatMeth2 Output

1. Alignment results

- Alignment sam or bam file;
  Here is a flagstat example of align bam file.

State Value
in total (QC-passed reads + QC-failed reads) 590045176 + 2351463
secondary 497310 + 4569
supplementary 0 + 0
duplicates 0 + 0
mapped (99.36% : 99.98%) 586287980 + 2351107
paired in sequencing 589547866 + 2346894
read1 294773933 + 1173447
read2 294773933 + 1173447
properly paired (97.01% : 0.00%) 571896886 + 0
with itself and mate mapped 585734494 + 2346182
singletons (0.01% : 0.02%) 56176 + 356
with mate mapped to a different chr 1411834 + 1764
with mate mapped to a different chr (mapQ>=5) 693127 + 455

The details please refer to :



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. Ref. PDF