Metaplot R script for WGBS

(100kb resolution)

Script (for Lansberg, chr3 only)

tair100kbbin_metaplot_Ler_chr3.R

Input file 1 (for Lansberg, chr3 only)

methratio_files.txt tab-delimited Ccount & CTcount over chromosomes, containing chromosome,start position, end position, Ccount, CTcount. Example file Ler1_total.bam_ler_chr3_100kb_CG.txt is shown below:

---

Chr	start	end	C_count	CT_count
ENA_LUHQ01000003_LUHQ01000003_1	1	100001	7723	61182
ENA_LUHQ01000003_LUHQ01000003_1	100001	200001	9276	57799
ENA_LUHQ01000003_LUHQ01000003_1	200001	300001	6864	66631
ENA_LUHQ01000003_LUHQ01000003_1	300001	400001	5763	63172

Input file 2 (for Lansberg, chr3 only)

configure_file.txt tab-delimited configure file contains the name of methratio_files.txt as well as the type (CG/CHG/CHH) and genotype of the methratio_files.txt. Example configure.txt is shown below:

---

Ler1_total.bam_ler_chr3_100kb_CG.txt	CG	ler	ler1
Ler1_total.bam_ler_chr3_100kb_CHG.txt	CHG	ler	ler1
Ler1_total.bam_ler_chr3_100kb_CHH.txt	CHH	ler	ler1

Output figure (for Lansberg, chr3 only)

metaplot over whole chromosome in pdf format. Example output is in Ler_100kb_metaplot.pdf.

Script (for fwa, chr1 to chr5)

tair100kbbin_metaplot_fwa.R

Input file 1 (for fwa, chr1 to chr5)

methratio_files.txt tab-delimited Ccount & CTcount over chromosomes, containing chromosome,start position, end position, Ccount, CTcount. Example file fwa_total.bam_tair10_100kb_CG.txt is shown below:

---

Chr	start	end	C_count	CT_count
chr1	0	100000	1272	43264
chr1	100000	200000	534	52396
chr1	200000	300000	2115	47835
chr1	300000	400000	238	46497
chr1	400000	500000	1458	48794

Input file 2 (for fwa, chr1 to chr5)

configure_file.txt tab-delimited configure file contains the name of methratio_files.txt as well as the type (CG/CHG/CHH) and genotype of the methratio_files.txt. Example configure_fwa.txt is shown below:

---

fwa_total.bam_tair10_100kb_CG.txt	CG	fwa	fwa
fwa_total.bam_tair10_100kb_CHG.txt	CHG	fwa	fwa
fwa_total.bam_tair10_100kb_CHH.txt	CHH	fwa	fwa

Output figure (for fwa, chr1 to chr5)

metaplot over whole chromosome in pdf format. Example output is in fwa_100kb_metaplot.pdf.