Question: Using Homer Programs For Denovo Motif : Different Results Among Its Own Versions
gravatar for RT
6.7 years ago by
RT10 wrote:

Hi Everyone,

I am trying my first hands-on with denovo motif discovery using HOMER. My sequence file has about 9K sequences that are 30bp each. I used two versions of the Homer programs for denovo motif finding and

-bash-3.2$ input.bed hg19 homer_output -bg background.bed -size given

-bash-3.2$ input.fasta fasta homer_output1 -fasta background.fasta

Firstly, number of results and reported match to the denovo motifs vary between both versions.!

I also used the " homer2 denovo " command and observed that the results are relatively consistent with only. I suspect that, when I give BED file, Homer fetches extra bp upstream and downstream from specified coordinate and So, I am getting a huge number of denovo motifs than the other two.

Is there any reason why the extra bp are required or significant in Homer? or Is there a way to make Homer only fetch the length I want using the BED file?

PS : I also used the - size option, but I don see any difference. From Homer manual -size option : if you wish to find motifs using your peaks using their exact sizes, use the option "-size given" However, for Transcription Factor peaks, most of the motifs are found +/- 50-75 bp from the peak center, making it better to use a fixed size rather than depend on your peak size.

Is there anything I am missing?I would appreciate any help with this.

bed • 3.7k views
ADD COMMENTlink written 6.7 years ago by RT10
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 814 users visited in the last hour