Changes between Version 12 and Version 13 of SOPs/enriched_tf_binding_sites

Timestamp:

11/05/20 08:59:26 (4 years ago)

Author:

gbell

Comment:

--

SOPs/enriched_tf_binding_sites

@@ -76 +76 @@
   * Public web site (older data): http://www.gene-regulation.com/cgi-bin/pub/programs/match/bin/match.cgi
 
-For position weight matrices (PWM) or regular expressions we can use programs like [[http://meme-suite.org/tools/mast|MAST]] or [[http://meme-suite.org/doc/fimo.html|FIMO]]. Most prediction programs have a setting to scan for TFBS for a given motif.  Example of a MAST command (where "MEME_motifs.txt" is a MEME-format file of TFBS motifs).
+For position weight matrices (PWM) or regular expressions we can use programs like [[http://meme-suite.org/tools/mast|MAST]] or [[http://meme-suite.org/doc/fimo.html|FIMO]]. 
+Most prediction programs have a setting to scan for TFBS for a given motif.  Be aware that these programs generally predict a large number of potential binding sites, many more than are likely to be functional, especially in one desired cell type.
+
+MAST can be run using its web  [[http://meme-suite.org/tools/mast|interface]] or from the [[http://meme-suite.org/doc/mast.html|command line]] using one or more motifs in MEME format on a set of sequences like this:
   
 {{{
-mast MEME_motifs.txt Promoters.fasta
+/usr/local/meme/bin/mast myMotifs.meme mySequences.fa
 }}}
 
-FIMO can be run using its web  [[http://meme-suite.org/doc/fimo.html|interface]] or from the [[http://meme-suite.org/doc/fimo.html?man_type=web|command line]] using a single motif in MEME format on a set of sequences like this:
+When running from the command line, MAST will create a directory called mast_out where it places its output.
+
+FIMO can be run using its web  [[http://meme-suite.org/doc/fimo.html|interface]] or from the [[http://meme-suite.org/doc/fimo.html?man_type=web|command line]] using one or more motifs in MEME format on a set of sequences like this:
 
 {{{
-fimo myMotif.meme mySequences.fa
+/usr/local/meme/bin/fimo myMotifs.meme mySequences.fa
 }}}