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).
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) |
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 |
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.) |
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 Relationships
Used by
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Current component
bedtools/bedtools_bed12tobed6biobox v0.4.2
Uses
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