How to retrieve the peak ID contributing to the motifs

[Emily E.T.]

I've inputted the fasta file of my chipseq peaks: column1: chr; 2:-50bp of summit; 3:+50bp of summit; 4:PeakID

 After I get the motif on MEME-ChIP, I tried to find what are the peakIDs(my column4 of input) that contribute to the motif, but then I click on the "Motif Sites in GFF3" under fimo in the MEME-ChIP HTML output the chr start end are outside of my input regions and doesnt show the peakIDs.  Is this a bug? And how could I find the peakIDs?

[cegrant]

Hi Emily,

The MEME Suite tools generally do very little parsing of the headers of FASTA files. Some of the tools (CREATE-PRIORS, FASTA-CENTER, FIMO, MCAST, MEME-ChIP, STREME, XSTREME) will parse UCSC and Galaxy header formats, but if the header is not in one of those two formats they will typically just take the header string up to the first white space as the name of the sequence and drop the rest. The coordinates will be assumed to start at position 1 at the first base in the sequence. If you want the coordinates reported by the MEME Suite tools to match the coordinates in you sequence headers, you'll have to convert your headers to use one of those two formats.

Charles

[Emily E.T.]

I see thanks!