Bismark(SE)
Introduction
This pipeline detect methylation site in CpG, ChG and CHH context. And get the region that is obviously different methylation rate among two samples.
| Input format | FASTQ(Illumina, IonTorrent, etc...) |
| Library layout | For paired-end read only |
| Species | Human(hg19) |
| Execution time | About 6 hours. (3M paired-end reads[36bp+36bp]) x 2 samples |
Pipeline history
Bismarkでマッピングを行いメチル化サイトを同定し、SAMtoolsのmpileupを用いてメチル化サイトの集計をします。
さらにフィッシャーの正確確率検定(FET)による二群間比較を行い、レポートで結果を報告します。
Inputs
FASTQ-formatted dna sequence file (paired-end)
read1
|
read2
| ||
FASTQ Format Specification
Outputs
２サンプル間でCpGアイランド毎のメチル化率を比較解析した結果レポート
Bismarkのメチル化検出結果（ゲノムビューワ表示）
Options
Comments
Use case
Related information
Public
| # | Tool name | Link to original site | Link to our wiki site |
| 1 | Bismark | (Original site) | (NGS surfer's wiki) |
| 2 | SAMtools | (Original site) | (NGS surfer's wiki) |
| 3 | BEDtools | (Original site) | (NGS surfer's wiki) |
Private
| # | Script name | Description | |
| 1 | bismarkSamToMetSamLike.pl | Forced to assign methylation information with ATGC to pile up by SAMtools | |
| 2 | callMethtlBaseFromMpiliup.pl | Convert pileupped ATGC to methylation count file | |
| 3 | bismarkSamToGeTsv.pl | Convert bismark output file to data for our genome browser: Genome Explorer | |
| 4 | convertMethylBasesInfToGeTsv.pl | Convert pileupped information to methylation rate track and methyl-C/non-metyl-C count track for Genome Explorer | |
| 5 | load_gbmap_data.pl | Load data for Genome Explorer | |
| 6 | mergeBasalVarInfToRegionalVarInf.sh | Merge two mathylation count files | |
| 7 | sumUpVarInfOutFromIntersec.pl | Sum up merged methylation count file per genomic features as like CpG island region information | |
| 8 | varRateTestWithFET.sh | Test two samples of methyl-C/non-methyl-C counts by FET:Fisher's Exact Test | |
| 9 | FETtestedRegionalVarInfToHtml.pl | Make HTML report to display the test result | |