bedtools/bedtools_makewindows

genomics

intervals

windows

tiling

sliding

binning

genome

segments

Description

Create adjacent or sliding windows across a genome or BED file.

This tool generates genomic windows either across entire chromosomes (using a genome file)
or within specific intervals (using a BED file). Windows can be fixed-size or variable-size,
and can be non-overlapping (adjacent) or overlapping (sliding). Useful for creating
genomic bins for analysis, tiling genomes, or generating sliding windows for statistics.

Type

bash_script

License

MIT

Keywords

genomics

intervals

windows

tiling

sliding

binning

genome

segments

Links

Repository

Documentation

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output: "$id.$key.output.bed"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.4.1 \  
  -main-script target/nextflow/bedtools/bedtools_makewindows/main.nf \  
  -params-file params.yaml

Input Options

Name	Type & Properties	Description
--genome -g	file	Genome file defining chromosome names and sizes. Format: Tab-delimited file with chromosome name and size Example line: chr1 249250621 Usage: Windows will be created for each chromosome in the file Sources: samtools faidx output or UCSC Table Browser
--input -b	file	BED file with genomic intervals. Format: BED file with chrom, start, end fields (minimum) Usage: Windows will be created for each interval in the file Alternative: Use instead of genome file to create windows within specific regions

Name

Type & Properties

--genome

-g

file

--input

-b

file

Outputs

Name	Type & Properties	Description
--output	file required output	Output file with generated windows. Format: BED format with chromosome, start, end coordinates Optional: Fourth column with window names (if ID naming option used) Sorting: Output is sorted by chromosome and start position

Name

Type & Properties

--output

file

required

output

Window Size Options

Name	Type & Properties	Description
--window_size -w	integer	Fixed window size in base pairs. Effect: Divide input intervals into fixed-sized windows Units: Base pairs (nucleotides) Usage: Cannot be used with --num_windows Example: 1000000 creates 1MB windows
--step_size -s	integer	Step size for sliding windows in base pairs. Default: Same as window size (non-overlapping windows) Effect: Distance between start positions of consecutive windows Usage: Must be used with --window_size Overlap: Window size minus step size gives overlap amount Example: With -w 1000 -s 500, creates 500bp overlapping windows
--num_windows -n	integer	Number of windows to create per input interval. Effect: Divide each interval into fixed number of windows Result: Window sizes vary to fit exactly within each interval Usage: Cannot be used with --window_size Example: 10 creates 10 equal-sized windows per interval

Name

Type & Properties

--window_size

-w

integer

--step_size

-s

integer

--num_windows

-n

integer

ID Naming Options

Name	Type & Properties	Description
--id_type -i	string	Add name column with specified ID type. Options: - `src`: Use source interval's name (requires named input intervals) - `winnum`: Use window number as ID (1, 2, 3, ...) - `srcwinnum`: Combine source name with window number (name_1, name_2, ...) Default: No name column (3 columns: chrom, start, end) With option: 4 columns including name column
--reverse	boolean_true	Reverse window numbering order. Effect: Report windows in decreasing numerical order Usage: Only applies when --id_type includes window numbering Example: With 3 windows, output 3, 2, 1 instead of 1, 2, 3 Default: false (ascending order)

Name

Type & Properties

--id_type

-i

string

--reverse

boolean_true