Package: methylmap
METHYLMAPMethylmap is a tool for visualization of modified nucleotide frequencies for large cohort sizes.EXAMPLEINPUT POSSIBILITIESSupported input possibilities are:BAM/CRAM files with MM and ML tags. Use --files input option.files from nanopolish (as processed by calculate_methylation_frequency.py). The methylation calls can additionally be phased using the available scripts in the "scripts" folder. Use --files input option.an own tab separtated table with nucleotide modification frequencies over all positions (methfreqtable), required header names are "chrom" (column with chromosome information) and "position" (columns with position information). Use --table input option. Example:chrom	position	sample_1	sample_2	sample_3	sample_4
0	chr1	100000.0	0.000	0.167	0.000	0.077
1	chr1	100000.5	0.000	0.000	0.100	0.000
2	chr1	100001.0	0.000	0.000	0.000	0.222
3	chr1	100002.0	0.000	0.000	0.000	0.000
4	chr1	100003.0	0.000	0.000	0.000	0.000a tab separated file with an overview table containing all nanopolish or BAM/CRAM files and their sample name and experimental group (header requires "path", "name" and "group"). Use --table input option. Example:path    name    group
0     /home/path_to_file/bamfile_sample_1.bam   samplename_1    case
1     /home/path_to_file/bamfile_sample_2.bam   samplename_2    control
2     /home/path_to_file/bamfile_sample_3.bam   samplename_3    control
3     /home/path_to_file/bamfile_sample_4.bam   samplename_4    caseINSTALLATIONpip install methylmapconda install -c bioconda methylmapUSAGEusage: methylmap [-h] (-f FILES [FILES ...] | -t TABLE) [-w WINDOW] [-n [NAMES ...]] [--gff GFF] [--expand EXPAND] 
[--outtable OUTTABLE] [--outfig OUTFIG] [--groups [GROUPS ...]] [-s] [--fasta FASTA] 
[--mod {5mC,5hmC,5fC,5caC,5hmU,5fU,5caU,6mA,5oxoG,Xao}] [--hapl] [--dendro] [-v]

Plotting tool for population scale nucleotide modifications.

options:
  -h, --help              show this help message and exit
  -f [FILES ...], --files [FILES ...]            
                          list with nanopolish (processed with calculate_methylation_frequency.py) files or BAM/CRAM files
  -t, --table             methfreqtable or overviewtable input
  -w, --window            region to visualise, format: chr:start-end (example: chr20:58839718-58911192)
  -n [NAMES ...], --names [NAMES ...]             
                          list with sample names
  --gff, --gtf            add annotation track based on GTF/GFF file
  --expand                number of base pairs to expand the window with in both directions
  --outtable              file to write the frequencies table to in tsv format
  --outfig                file to write output heatmap to, default: methylmap_{chr}_{start}_{end}.html (missing paths will be created)
  --groups [GROUPS ...]                
                          list of experimental group for each sample
  -s, --simplify          simplify annotation track to show genes rather than transcripts
  --fasta                 fasta reference file, required when input is BAM/CRAM files or overviewtable with BAM/CRAM files
  --hapl                  display modification frequencies in input BAM/CRAM file for each haplotype (alternating haplotypes in methylmap)
  --mod {5mC,5hmC,5fC,5caC,5hmU,5fU,5caU,6mA,5oxoG,Xao}                  
                          modified base of interest when BAM/CRAM files as input. Options are: 5mC, 5hmC, 5fC, 5caC, 5hmU, 5fU, 5caU, 6mA, 5oxoG, Xao, default = 5mC
  --dendro                perform hierarchical clustering on the samples/haplotypes and visualize with dendrogram on sorted heatmap as output
  -v, --version           print version and exitMORE INFORMATIONMore information:https://www.biorxiv.org/content/10.1101/2022.11.28.518239v1