Zero peaks detected using findMotifsGenome.pl

Question

[ichmagbaeume]

Hi,

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!

[ATpoint]

I am pretty sure the mm10 reference the Homer uses by default assumes chromosome names with the chr prefix rather than plain numbers. Try to save it as BED and add chr to column1. Be sure the file is tab-separated and without a header.

Answer 1

[SilviaT]

Hey! My reply comes a little late, but maybe it could help someone else reading this post....

I had the same problem: after extracting the genomic coordinates of a list of genes using biomaRt (in R) and exporting data it to a .txt file, Homer wouldn't recognise any peaks. This is how the file looked:

ENSG00000209082,MT,3230,3304,1

ENSG00000198888,MT,3307,4262,1

I solved the problem formatting it like this:

ENSG00000209082 chrM 3230 3304 +

ENSG00000198888 chrM 3307 4262 +

Where each value is separated by a tab.

Hope this helps :)