Galaxy |

bedtools getfasta (version 2.30.0+galaxy1)

BED/bedGraph/GFF/VCF/EncodePeak file:

Choose the source for the FASTA file:

FASTA file:

Use the 'name' column in the BED file and the coordinates for the FASTA headers in the output FASTA file:

Use the 'name' column in the BED file for the FASTA headers in the output FASTA file:

Report extract sequences in a tab-delimited format instead of in FASTA format:

Force strandedness:

If the feature occupies the antisense strand, the sequence will be reverse complemented

Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage.:

If set, the coverage will be calculated based the spliced intervals only. For BAM files, this inspects the CIGAR N operation to infer the blocks for computing coverage. For BED12 files, this inspects the BlockCount, BlockStarts, and BlockEnds fields (i.e., columns 10,11,12). If this option is not set, coverage will be calculated based on the interval's START/END coordinates, and would include introns in the case of RNAseq data.

What it does

bedtools getfasta 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>”.

The headers in the input FASTA file must exactly match the chromosome column in the BED file.
You can use the UNIX fold command to set the line width of the FASTA output. For example, fold -w 60 will make each line of the FASTA file have at most 60 nucleotides for easy viewing.

This tool is part of the bedtools package from the Quinlan laboratory.

Citation

If you use this tool in Galaxy, please cite:

Bjoern A. Gruening (2014), Galaxy wrapper