bedtools/bedtools_bed12tobed6

Converts

BED12

BED6

Description

Converts BED features in BED12 (a.k.a. “blocked” BED features such as genes) to discrete BED6 features.
For example, in the case of a gene with six exons, bed12ToBed6 would create six separate BED6 features (i.e., one for each exon).

Type

bash_script

License

MIT

Keywords

Converts

BED12

BED6

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.bed6"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.4.2 \  
  -main-script target/nextflow/bedtools/bedtools_bed12tobed6/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input -i	file required	Input BED12 file containing blocked features. Requirements: - Must be in BED12 format (12 columns) - Should contain blocked features (e.g., genes with exons) - Blocks are defined by columns 10-12 (blockCount, blockSizes, blockStarts)

Name

Type & Properties

--input

-i

file

required

Outputs

Name	Type & Properties	Description
--output -o	file output	Output BED6 file containing discrete features. Output format: - Each block from input BED12 becomes a separate BED6 entry - Maintains chromosome, strand, and name information - Coordinates are adjusted to represent individual blocks

Name

Type & Properties

--output

-o

file

output

Options

Name	Type & Properties	Description
--n_score -n	boolean_true	Force the score to be the 1-based block number from the BED12. Default behavior: Preserves original score from BED12 With --n_score: Sets score to block number (1, 2, 3, etc.)

Name

Type & Properties

--n_score

-n

boolean_true