ceqlogo error "No motifs were specified"

[Arun Prasanna]

Hi,

I tried to create logos with ceqlogo. My input is motif file with 30 motifs in minimal MEME format. With the following command, I got "No motifs specified".  Can anyone help ?

./ceqlogo -i MEME.meme-io -o logo.eps -f EPS. 

Thanks.

[CharlesEGrant]

Here is the documentation for the ceqlogo command: http://meme-suite.org/doc/ceqlogo.html

You have to specify which motifs in a file you  want to create logograms for.  You can do this using the '-m' or the '-i' command line options:

ceqlogo -i2  chen2008.meme  -o logo.eps

ceqlogo -iCTCF  chen2008.meme  -o logo.eps

or 

ceqlogo -i chen2008.meme -m1   -o logo.eps

ceqlogo -i chen2008.meme -mCTCF   -o logo.eps

Notice that you can specify the motif using its  ordinal index in the file, or the name given on the MOTIF line.

If you want to create a logogram for multiple motifs you can repeat the arguments:

 

ceqlogo -i2  chen2008.meme -i3 chen2008.meme  -o logo.eps

ceqlogo -i chen2008.meme -m1   -m2 -o logo.eps