Motif finding with HOMER

Question

[biostart]

Hello,

I am using HOMER for motif discivery from ChIP-seq. Everything is fine, except that all links in the HTML file with results are broken. The PNG or PDF files linked from the HTML do not exist. Anyone else encountered this problem? Any solutions?

Thanks!

[fanli.gcb]

Did you also grab the homerResults/ and knownResults/ directories from the output folder? The images linked in the HTML are located in those places...

[biostart]

Of course I checked all the folders. HOMER does not generate any PNG or PDF files :(

[xiaofeiwang198266]

Did you figure out your problems? I got same problem. (I used it many years ago, it worked well but now, I did not make it work. I see this "Sequence logos produced during motif finding are now rendered using SVG instead of relying on weblogo/ghostscript." http://homer.ucsd.edu/homer/. But, I did not get what does that mean exactly, what else dependency I need to install?)

[xiaofeiwang198266]

answer the problem just for people who got same problem: Figure the problem out by installing weblogs and newer version of Ghostscript (9.10).

Answer 1

[biostart]

P.S. It seems that HOMER requires a third-party program seqlogo which needs to be installed separately. I guess this is the problem