甲基化数据下游分析及可视化

2024-07-12 18:26| 来源: 网络整理| 查看: 265

multiqc_reportbismark_reportbismark_summary_report

全基因组甲基化水平分析(胞嘧啶碱基的甲基化水平)

通常CG甲基化存在于基因和重复序列中，在基因表达调控过程中起到非常重要的作用。非CG类型的序列（CHG和CHH）在基因中非常少见，主要存在于基因间区和含重复序列的区域，在沉默转座子过程中起关键作用。

样本A全基因组各类调控元件范围内的甲基化水平

全基因组甲基化数据分布趋势甲基化 C 碱基中 CG,CHG,与 CHH 的分布比例

mCG、mCHG 和 mCHH 三种碱基类型的构成比例在不同物种中,甚至是同一物种不同样品中都存在很大差异。因此,不同时间、空间、生理条件下的样品会表现出不同的甲基化图谱,各类 mC(mCG、mCHG 和,mCHH)的数目,及其在全部 mC 的位点中所占的比例,在一定程度上反应了特定物种的全基因组甲基化图谱特征。mCG、mCGH 和 mCHH 分别表示甲基化 CG、甲基化 CHG 和甲基化 CHH。三种碱基类型占比总和为 100%。

样本A中 mCG、mCHG 和 mCHH三种类型甲基化胞嘧啶的比例

样本A中 mCG、mCHG 和 mCHH 三种类型甲基化胞嘧啶的分布

Bismark report for: trimmed/test_R1_trim.fq.gz and trimmed/test_R2_trim.fq.gz (version: v0.22.1) Bismark was run with Bowtie 2 against the bisulfite genome of /data/wangyang/snakemake-bisulfite/data2/index/ with the specified options: -q --score-min L,0,-0.2 -p 3 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Option '--non_directional' specified: alignments to all strands were being performed (OT, OB, CTOT, CTOB) Final Alignment report ====================== Sequence pairs analysed in total: 5000 Number of paired-end alignments with a unique best hit: 4619 Mapping efficiency: 92.4% Sequence pairs with no alignments under any condition: 0 Sequence pairs did not map uniquely: 381 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 2323 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 2296 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 231335 Total methylated C's in CpG context: 52326 Total methylated C's in CHG context: 1132 Total methylated C's in CHH context: 2039 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 15754 Total unmethylated C's in CHG context: 56443 Total unmethylated C's in CHH context: 103641 Total unmethylated C's in Unknown context: 0 C methylated in CpG context: 76.9% C methylated in CHG context: 2.0% C methylated in CHH context: 1.9% Can't determine percentage of methylated Cs in unknown context (CN or CHN) if value was 0 Bismark completed in 0d 0h 0m 10s test_MappedOn_NC010473_trim_bismark_pe.deduplicated.sorted.bam Parameters used to extract methylation information: Bismark Extractor Version: v0.22.1 Bismark result file: single-end (SAM format) Output specified: comprehensive Processed 9238 lines in total Total number of methylation call strings processed: 9238 Final Cytosine Methylation Report ================================= Total number of C's analysed: 231335 Total methylated C's in CpG context: 52326 Total methylated C's in CHG context: 1132 Total methylated C's in CHH context: 2039 Total C to T conversions in CpG context: 15754 Total C to T conversions in CHG context: 56443 Total C to T conversions in CHH context: 103641 C methylated in CpG context: 76.9% C methylated in CHG context: 2.0% C methylated in CHH context: 1.9% CG、CHG 和 CHH 中的所有 C 的甲基化水平

不同类型的 C 碱基（CG、CHG 和 CHH）, 其甲基化水平在不同物种间，甚至同一物种不同细胞类型不同条件下其甲基化水平都存在差。计每种类型（CG、CHG 和 CHH）甲基化 C 的甲基化水平分布，反应了该物种 DNA 甲基化特征。

甲基化 C 的甲基化水平

图中x轴表示甲基化水平，y轴表示特定甲基化水平的胞嘧啶碱基在所有甲基化碱基中所占的比例

test2.myCpG.txt

chrBasechrbasestrandcoveragefreqCfreqT chr21.9764513chr219764513R207525 chr21.9764539chr219764539R20955 chr21.9767701chr219767701F101090 chr21.9804584chr219804584F109010 chr21.9804595chr219804595F101000 chr21.9802620chr219802620F1361.5438.46 library(methylKit) file.list=list( system.file("extdata", "test1.myCpG.txt", package = "methylKit"), system.file("extdata", "test2.myCpG.txt", package = "methylKit"), system.file("extdata", "control1.myCpG.txt", package = "methylKit"), system.file("extdata", "control2.myCpG.txt", package = "methylKit") ) myobj=methRead(file.list, sample.id=list("test1","test2","ctrl1","ctrl2"), assembly="hg18", treatment=c(1,1,0,0), context="CpG", mincov = 10) png(file="a.png") getMethylationStats(myobj[[2]],plot=TRUE,both.strands=FALSE) dev.off()

library(tidyverse) myCpG

【本文地址】

甲基化数据下游分析及可视化

甲基化数据下游分析及可视化

今日新闻

推荐新闻