Question: Get fasta file from peak called BED file to do Motif analysis
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gravatar for reubenmcgregor88
20 months ago by
reubenmcgregor8850 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?

ADD COMMENTlink written 20 months ago by reubenmcgregor8850
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