5.11 fastaFromBed

fastaFromBed extracts sequences from a FASTA file for each of the intervals defined in a BED file. The headers in the input FASTA file must exactly match the chromosome column in the BED file.

5.11.1 Usage and option summary

Usage:

fastaFromBed [OPTIONS] -fi <input FASTA> -bed <BED/GFF/VCF> -fo <output FASTA>

Option	Description
-name	Use the “name” column in the BED file for the FASTA headers in the output FASTA file.
-tab	Report extract sequences in a tab-delimited format instead of in FASTA format.
-s	Force strandedness. If the feature occupies the antisense strand, the sequence will be reverse complemented. Default: strand information is ignored.

5.11.2 Default behavior

fastaFromBed will extract the sequence defined by the coordinates in a BED interval and create a new FASTA entry in the output file for each extracted sequence. By default, the FASTA header for each extracted sequence will be formatted as follows: “<chrom>:<start>-<end>”.

For example:

$ cat test.fa
>chr1
AAAAAAAACCCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG

cat test.bed
chr1 5 10

fastaFromBed -fi test.fa -bed test.bed -fo test.fa.out

cat test.fa.out
>chr1:5-10
AAACC

5.11.3 Using the BED “name” column as a FASTA header.

Using the -name option, one can set the FASTA header for each extracted sequence to be the “name” columns from the BED feature.

For example:

cat test.fa
>chr1
AAAAAAAACCCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG

cat test.bed
chr1 5 10 myseq

fastaFromBed -fi test.fa -bed test.bed -fo test.fa.out -name

cat test.fa.out
>myseq
AAACC

5.11.4 Creating a tab-delimited output file in lieu of FASTA output.

Using the -tab option, the -fo output file will be tab-delimited instead of in FASTA format.

For example:

cat test.fa
>chr1
AAAAAAAACCCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG

cat test.bed
chr1 5 10 myseq

fastaFromBed -fi test.fa -bed test.bed -fo test.fa.out.tab -name -tab

cat test.fa.out
myseq AAACC

5.11.5 (-s)Forcing the extracted sequence to reflect the requested strand

fastaFromBed will extract the sequence in the orientation defined in the strand column when the “-s” option is used.

For example:

cat test.fa
>chr1
AAAAAAAACCCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG

cat test.bed
chr1 20 25 forward 1 +
chr1 20 25 reverse 1 -

fastaFromBed -fi test.fa -bed test.bed -s -name -fo test.fa.out

cat test.fa.out
>forward
CGCTA
>reverse
TAGCG