I am extremely new to this, so apologies in advance for any mistakes in my post!
I am trying to use findMotifsGenome.pl in Homer to identify transcription factor motifs based on genomic coordinates, but I always get a message that no peaks are detected. I've tried various different input files. One example is:
Chr Start End PeakID Strand
1 107804574 107805846 chr1-1 +
1 108175088 108175571 chr1-2 +
1 109813645 109814197 chr1-3 +
1 120354898 120355172 chr1-4 +
1 129885964 129887418 chr1-5 +
1 132716813 132717831 chr1-6 +
1 135963662 135964206 chr1-7 +
1 136085513 136086199 chr1-8 +
1 138027497 138028456 chr1-9 +
1 138033620 138034057 chr1-10 +
1 138116297 138117672 chr1-11 +
I've also tried saving it as both a bed and txt file, but I can't seem to find a format that works. This is what I get as output:
Position file = final_sig_coordinates.bed Genome = mm10 Output Directory = Results/ Fragment size set to 100 Will use repeat masked sequences Found mset for "mouse", will check against vertebrates motifs Peak/BED file conversion summary: BED/Header formatted lines: 0 peakfile formatted lines: 0
Peak File Statistics: Total Peaks: 0 Redundant Peak IDs: 0 Peaks lacking information: 0 (need at least 5 columns per peak) Peaks with misformatted coordinates: 0 (should be integer) Peaks with misformatted strand: 0 (should be either +/- or 0/1) Only 0 peaks found! If many more expected, maybe the file format is for Macs only Try running the command: changeNewLine.pl "Results//target.clean..pos"
It seems to run, but I get no output. I have not been able to use the command it tells me to try, either. Can anyone help? Is it a formatting issue? A file issue?
Again, apologies if this is a really stupid question or if this post is formatted incorrectly! Thank you!