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.

Type

bash_script

License

GPL-2.0

Keywords

sequencing

fasta

BED

GFF

VCF

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"  
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

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.

Name

Type & Properties

--input_fasta

file

--input_bed

file

--rna

boolean_true

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.

Name

Type & Properties

--strandedness

-s

boolean_true

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.

Name

Type & Properties

--output

-o

file

required

output

--tab

boolean_true

--bed_out

boolean_true

--name

boolean_true

--name_only

boolean_true

--split

boolean_true

--full_header

boolean_true