https://divingintogeneticsandgenomics.com/tags/motif/ Recent content in Motif on Chatomics Hugo -- gohugo.io en-us © 2018 Ming 'Tommy' Tang Thu, 13 Feb 2014 07:13:00 -0800 https://divingintogeneticsandgenomics.com/archive/how-to-get-a-genome-wide-motif-bed-file/ Thu, 13 Feb 2014 07:13:00 -0800 https://divingintogeneticsandgenomics.com/archive/how-to-get-a-genome-wide-motif-bed-file/ Someone was asking this question on Seqanswers http://seqanswers.com/forums/showthread.php?t=40762&highlight=genome+motif+bed For motif analysis, the most popular program is MEME http://meme.nbcr.net/meme/ There are a bunch of tools in the suites including some useful ones for ChIP-seq I also saw RAST http://rsat01.biologie.ens.fr/rsa-tools/index.html and oPOSSUM were mentioned http://opossum.cisreg.ca/oPOSSUM3/ I analyze ChIP-seq data a lot. Usually, one gets a bed file containing the positions of the peaks. However, many motif analysis programs require fasta file as input.