Question: Get fasta file from peak called BED file to do Motif analysis
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reubenmcgregor88 • 50 wrote:
Hi all,
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?