## METHYLMAP
Methylmap is a tool for visualization of modified nucleotide frequencies for large cohort sizes.
### EXAMPLE
### INPUT POSSIBILITIES
Supported 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 0.000
```
- a 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 case
````
### INSTALLATION
pip install methylmap
conda install -c bioconda methylmap
### USAGE
```
usage: 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 exit
```
### MORE INFORMATION
More information: https://www.biorxiv.org/content/10.1101/2022.11.28.518239v1
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"description": "## METHYLMAP\n\nMethylmap is a tool for visualization of modified nucleotide frequencies for large cohort sizes. \n\n### EXAMPLE\n\n \n\n### INPUT POSSIBILITIES\n\nSupported input possibilities are:\n\n- BAM/CRAM files with MM and ML tags. Use --files input option.\n\n- 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.\n\n- 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:\n```\n\tchrom\tposition\tsample_1\tsample_2\tsample_3\tsample_4\n0\tchr1\t100000.0\t0.000\t0.167\t0.000\t0.077\n1\tchr1\t100000.5\t0.000\t0.000\t0.100\t0.000\n2\tchr1\t100001.0\t0.000\t0.000\t0.000\t0.222\n3\tchr1\t100002.0\t0.000\t0.000\t0.000\t0.000\n4\tchr1\t100003.0\t0.000\t0.000\t0.000\t0.000\n```\n\n- a 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:\n```\n path name group\n0 /home/path_to_file/bamfile_sample_1.bam samplename_1 case\n1 /home/path_to_file/bamfile_sample_2.bam samplename_2 control\n2 /home/path_to_file/bamfile_sample_3.bam samplename_3 control\n3 /home/path_to_file/bamfile_sample_4.bam samplename_4 case\n````\n\n### INSTALLATION\n\npip install methylmap\n\nconda install -c bioconda methylmap\n\n### USAGE\n\n```\nusage: methylmap [-h] (-f FILES [FILES ...] | -t TABLE) [-w WINDOW] [-n [NAMES ...]] [--gff GFF] [--expand EXPAND] \n[--outtable OUTTABLE] [--outfig OUTFIG] [--groups [GROUPS ...]] [-s] [--fasta FASTA] \n[--mod {5mC,5hmC,5fC,5caC,5hmU,5fU,5caU,6mA,5oxoG,Xao}] [--hapl] [--dendro] [-v]\n\nPlotting tool for population scale nucleotide modifications.\n\noptions:\n -h, --help show this help message and exit\n -f [FILES ...], --files [FILES ...] \n list with nanopolish (processed with calculate_methylation_frequency.py) files or BAM/CRAM files\n -t, --table methfreqtable or overviewtable input\n -w, --window region to visualise, format: chr:start-end (example: chr20:58839718-58911192)\n -n [NAMES ...], --names [NAMES ...] \n list with sample names\n --gff, --gtf add annotation track based on GTF/GFF file\n --expand number of base pairs to expand the window with in both directions\n --outtable file to write the frequencies table to in tsv format\n --outfig file to write output heatmap to, default: methylmap_{chr}_{start}_{end}.html (missing paths will be created)\n --groups [GROUPS ...] \n list of experimental group for each sample\n -s, --simplify simplify annotation track to show genes rather than transcripts\n --fasta fasta reference file, required when input is BAM/CRAM files or overviewtable with BAM/CRAM files\n --hapl display modification frequencies in input BAM/CRAM file for each haplotype (alternating haplotypes in methylmap)\n --mod {5mC,5hmC,5fC,5caC,5hmU,5fU,5caU,6mA,5oxoG,Xao} \n modified base of interest when BAM/CRAM files as input. Options are: 5mC, 5hmC, 5fC, 5caC, 5hmU, 5fU, 5caU, 6mA, 5oxoG, Xao, default = 5mC\n --dendro perform hierarchical clustering on the samples/haplotypes and visualize with dendrogram on sorted heatmap as output\n -v, --version print version and exit\n ```\n\n### MORE INFORMATION\n\nMore information: https://www.biorxiv.org/content/10.1101/2022.11.28.518239v1\n\n",
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