bedtools/bedtools_getfasta
sequencing
fasta
BED
GFF
VCF
Description
Extract sequences from a FASTA file for each of the intervals defined in a BED/GFF/VCF file.
Input arguments
Name | Type & Properties | Description |
|---|---|---|
--input_fasta | file | FASTA file containing sequences for each interval specified in the input BED file. The headers in the input FASTA file must exactly match the chromosome column in the BED file. |
--input_bed | file | BED file containing intervals to extract from the FASTA file. BED files containing a single region require a newline character at the end of the line, otherwise a blank output file is produced. |
--rna | boolean_true | The FASTA is RNA not DNA. Reverse complementation handled accordingly. |
Run arguments
Name | Type & Properties | Description |
|---|---|---|
--strandedness -s | boolean_true | Force strandedness. If the feature occupies the antisense strand, the output sequence will be reverse complemented. By default strandedness is not taken into account. |
Output arguments
Name | Type & Properties | Description |
|---|---|---|
--output -o | file required output | Output file where the output from the 'bedtools getfasta' commend will be written to. |
--tab | boolean_true | Report extract sequences in a tab-delimited format instead of in FASTA format. |
--bed_out | boolean_true | Report extract sequences in a tab-delimited BED format instead of in FASTA format. |
--name | boolean_true | Set the FASTA header for each extracted sequence to be the "name" and coordinate columns from the BED feature. |
--name_only | boolean_true | Set the FASTA header for each extracted sequence to be the "name" columns from the BED feature. |
--split | boolean_true | When --input is in BED12 format, create a separate fasta entry for each block in a BED12 record, blocks being described in the 11th and 12th column of the BED. |
--full_header | boolean_true | Use full fasta header. By default, only the word before the first space or tab is used. |
Run this component
Run the following command to execute this component with Nextflow:
cat > params.yaml <<'EOM'
output: "$id.$key.output"
id: "run"
publish_dir: "output/"
EOM
nextflow run https://packages.viash-hub.com/vsh/biobox.git \
-revision v0.3.0 \
-main-script target/nextflow/bedtools/bedtools_getfasta/main.nf \
-params-file params.yaml Relationships
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Current component
bedtools/bedtools_getfastabiobox v0.3.0
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