Location of motif

[Priyanka Raina]

Hi,

After meme, how can I know the position of known motifs in the genome. I want to make a SNP bed file from the same to run motifbreakR.

Thank you

  

[cegrant]

FIMO can be used to scan a sequence database for matches to motifs identified by MEME. Documentation for FIMO can be found here, here, and here. FIMO provide output in XML, HTML, plain text, and GFF3 format. You'd have to write your own script to convert it to BED format.