Question: Can't find documentation about output of homer2 find command
gravatar for colin.kern
10 weeks ago by
United States
colin.kern900 wrote:

I have a set of short sequences obtained from doing DNase footprinting and I want to filter them by removing sequences that don't contain a known TF motif. I have done this with FIMO but we have decided to use Homer for doing motif enrichment rather than MEME, so I want to do the filtering with Homer too if possible. I used the "homer2 find" command which I found mentioned in the documentation here, but with no explanation of how to use it or what the output means. I figured out how to use it by just typing "homer2 find" without any arguments which printed some usage information, so I have the output now which looks like this:

chr9:104478785-104478824        -12     TBGCACGCAA      Arnt:Ahr(bHLH)/MCF7-Arnt-ChIP-Seq(Lo_et_al.)/Homer      +       -0.357320
chr9:104478678-104478724        11      TBGCACGCAA      Arnt:Ahr(bHLH)/MCF7-Arnt-ChIP-Seq(Lo_et_al.)/Homer      +       3.356042
chr9:104478785-104478824        6       CCAGGAACAG      AR-halfsite(NR)/LNCaP-AR-ChIP-Seq(GSE27824)/Homer       +       -1.818086
chr9:104478678-104478724        -6      CCAGGAACAG      AR-halfsite(NR)/LNCaP-AR-ChIP-Seq(GSE27824)/Homer       +       8.129395
chr9:104478503-104478532        -5      CCAGGAACAG      AR-halfsite(NR)/LNCaP-AR-ChIP-Seq(GSE27824)/Homer       -       -5.348250
chr9:104478095-104478123        -9      CCAGGAACAG      AR-halfsite(NR)/LNCaP-AR-ChIP-Seq(GSE27824)/Homer       +       -1.677003

It seems like the last column is probably some kind of significance score, but I'm not sure how to interpret it. Since it has both positive and negative values, I don't see how it could be something like a log p-value, so I'm not sure what it is exactly and what cut-off might be appropriate, or whether it actually has nothing to do with significance. Is anyone familiar with this output or knows where the documentation for it might be?

motif enrichment homer • 85 views
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