(100kb resolution)
tair100kbbin_metaplot_Ler_chr3.R
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
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
metaplot over whole chromosome in pdf format. Example output is in Ler_100kb_metaplot.pdf.
tair100kbbin_metaplot_fwa.R
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
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
metaplot over whole chromosome in pdf format. Example output is in fwa_100kb_metaplot.pdf.