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bedtools MaskFastaBed (version 2.30.0)

BED/bedGraph/GFF/VCF/EncodePeak file:

FASTA file:

Soft-mask (that is, convert to lower-case bases) the FASTA sequence:

By default, hard-masking (that is, conversion to Ns) is performed

Replace masking character:

That is, instead of masking with Ns, use another character

Use full fasta header.:

By default, only the word before the first space or tab is used

What it does

bedtools maskfasta masks sequences in a FASTA file based on intervals defined in a feature file. The headers in the input FASTA file must exactly match the chromosome column in the feature file. This may be useful fro creating your own masked genome file based on custom annotations or for masking all but your target regions when aligning sequence data from a targeted capture experiment.

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