local-methylation-profile

To visualize local DNA methylation profiles around transcription start sites, provide a methylation BED file and a target regions BED file. The tool bins methylation data around the specified regions and outputs a profile TSV and a plot showing mean and standard error.

Methylation and target region files should be in BED format for generating a methylation profile plot. You will be prompted to specify the exact column indices for methylation fraction and coverage during the analysis to ensure accurate aggregate visualization.

Yes, you can aggregate average methylation patterns around specific genomic peaks. By providing target regions like TF peaks or promoters in a BED file, the tool calculates mean methylation with standard error across fixed bins and generates a visualization plot.

Yes, you must manually specify methylation fraction columns when analyzing BED files. The tool always prompts for the exact column indices for methylation fraction or percentage and never decides automatically, ensuring correct data mapping for the aggregate profile.

The outputs generated from a local methylation profile analysis include a profile TSV file and a plot image. The plot visualizes the mean methylation pattern with a center line and a ribbon representing standard error across the binned flanking regions.