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 :