Question: Motif finding with HOMER
0
gravatar for biostart
3.3 years ago by
biostart340
Germany
biostart340 wrote:

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!

sequencing motif pwm chip-seq • 1.4k views
ADD COMMENTlink written 3.3 years ago by biostart340

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

ADD REPLYlink written 3.3 years ago by fanli.gcb690

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

ADD REPLYlink written 3.3 years ago by biostart340

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?)

ADD REPLYlink written 2.8 years ago by xiaofeiwang19826620

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

ADD REPLYlink written 2.8 years ago by xiaofeiwang19826620
0
gravatar for biostart
3.3 years ago by
biostart340
Germany
biostart340 wrote:

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

ADD COMMENTlink written 3.3 years ago by biostart340
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