I have some called peaks in BED format and would like to extract the sequences in a FASTA format in order to do Motif analysis on the regions.
I have tried to use the "getfastabed" BEDtool but even though the tool claims to do the following:
bedtools getfasta will extract the sequence defined by the coordinates in a BED interval and create a new FASTA
It needs a FASTA file as an input.
Does anyone know how to use this tool? OR how to perform motif scanning on BED files?