MEMECHIP: Run MEME, DREME, TOMTOM and some other MEME Suite programs on ChIP-seq data Options: -upmotif uploaded motifs -bfile specifiy a background file -norc search the given strand only. -help brief help message MEME Specific Options: -meme-mod [oops|zoops|anr] sites used in a single sequence -meme-minw minimum motif width -meme-maxw maximum motif width -meme-nmotifs maximum number of motifs to find -meme-minsites minimum number of sites per motif -meme-maxsites maximum number of sites per motif -meme-pal look for palindromes only DREME Specific Options: -dreme-e maximum motif E-value -dreme-m maximum number of motifs to find CentriMo Specific Options: -centrimo-local compute enrichment of all regions (not only central) -centrimo-score minimum match score -centrimo-maxreg maximum central enrichment region -centrimo-ethresh threshold for reporting enrichment -centrimo-noseq don't store sequence ids in output Motif Databases The motif databases may be specified as a pattern using * as a wildcard. Outputs to the directory that it is run in. ]]> norc -norc false Runs MEME, DREME and CentriMo on given strand only meme-pal -meme-pal false MEME only looks for palindromes centrimo-local -centrimo-local false CentriMo tests all regions centrimo-noseq -centrimo-noseq false CentriMo does not include sequence list bfile -bfile FILE INPUT false Background File upmotif -upmotif FILE INPUT false Uploaded Motif Database File meme-mod -meme-mod STRING oops zoops anr zoops true MEME Site Selection Mode meme-minw -meme-minw INT 6 true MEME minimum motif width meme-maxw -meme-maxw INT 30 true MEME maximum motif width meme-nmotifs -meme-nmotifs INT 3 true MEME number of motifs meme-minsites -meme-minsites INT false MEME minimum sites per motif meme-maxsites -meme-maxsites INT false MEME maximum sites per motif dreme-e -dreme-e FLOAT false DREME E-value threshold dreme-m -dreme-m INT 10 false DREME maximum number of motifs centrimo-score -centrimo-score FLOAT false CentriMo minimum site score centrimo-maxreg -centrimo-maxreg INT 200 false Maximum enrichment region size centrimo-ethresh -centrimo-ethresh FLOAT false CentriMo E-value threshold sequences FILE INPUT true ChIP-seq Site Sequences dbs STRING true Motif Databases Pattern @SERVICE_DIR@/meme-chip_webservice false