18. beta_profile_region

18.1. Overview

beta_profile_region generates a strand-aware DNA methylation profile across user-defined genomic regions and their upstream/downstream flanks.

Profiles are normalized and oriented 5’ to 3’ relative to the strand of each target region. Three profile groups are reported:

upstream flank
target region
downstream flank

18.2. Input Files

18.2.1. Methylation file

The methylation input must be BED6 or BED6+ with Beta-values in column 5.

The first six columns are expected to represent:

chrom, start, end, name, Beta_value, strand

Example:

chr22   44021512    44021513    cg24055475    0.9231    -
chr13   111568382   111568383   cg06540715    0.1071    +
chr20   44033594    44033595    cg21482942    0.6122    -

Compressed input is supported when supported by the CpGtools reader.

18.2.2. Region file

The target-region input must be BED3 or BED3+. If column 6 is present, it is used as the strand. If strand is absent or is not + or -, the region is treated as being on the + strand.

Example:

chr1    15864    15865
chr1    18826    18827
chr1    29406    29407

Exact duplicate target intervals are removed while preserving input order.

18.3. Usage

Basic usage:

beta_profile_region \
    -r hg19.RefSeq.union.1Kpromoter.bed.gz \
    -i test_02.bed6.gz \
    -o region_profile

By default, 2,000 bp are profiled upstream and downstream of each target region.

Useful options include:

-u, --upstream – upstream flank length in bp (default: 2000)
-d, --downstream – downstream flank length in bp (default: 2000)
--format {png,pdf,both} – plot output format (default: pdf)
--dpi – PNG resolution (default: 300)
--width – plot width in inches (default: 8)
--height – plot height in inches (default: 5)
--no_plot – write the profile table without generating a plot
-o, --out_prefix, --output – output prefix

Display all options with:

beta_profile_region -h

18.4. Output

For output prefix region_profile, the command always writes:

region_profile.region_profile.tsv – normalized methylation profile

The table contains:

Group – Upstream_region, User_region, or Downstream_region
Relative_position(5'->3') – normalized position within each profile group
Average_beta – average methylation value

Unless --no_plot is used, the command also writes one or more plots:

region_profile.region_profile.pdf
region_profile.region_profile.png

Use --format both to generate both plot formats.