Utilities / FASTA from BED

Description

Extract DNA sequences into a fasta file based on feature coordinates.

Parameters

• Use the name field for the FASTA header (yes, no) [no]
• Write output in TAB delimited format (yes, no) [no]
• Force strandedness (yes, no) [no]

Details

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.

Output

The output is a fasta-format sequence file.

References

This tool uses the BEDTools package. Please cite the article:

Quinlan AR and Hall IM, 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 26, 6, pp. 841–842.

Please see the BEDTools homepage for more details.