Changes between Version 10 and Version 11 of SOPs/enriched_tf_binding_sites

Timestamp:

11/04/20 14:55:43 (4 years ago)

Author:

gbell

Comment:

--

SOPs/enriched_tf_binding_sites

@@ -59 +59 @@
        * TFBS prediction programs.
   
-Depending on the source of the motif, the program used to scan for potential binding sites may be different.
+Depending on the source of the motif file, the program used to scan for potential binding sites may be different:
+* MEME-format files can be found in /nfs/BaRC_datasets/MEME_matrix_databases
+* TRANSFAC-format files can be found in /nfs/BaRC_datasets/Transfac
 
 [http://gene-regulation.com/Match_command_line.txt TRANSFAC's match] - for transcription factor binding sites
   * commercial application requiring a license for the most up-to-date version
-  * Whitehead only: See BaRC_datasets/Transfac for the command-line program and (old) data files
+  * Whitehead only: See BaRC_datasets/Transfac for the command-line program and (old) data files such as the PRF files with matrix subsets of different types.
 {{{
 # Search using all Transfac profiles
@@ -74 +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 MAST. Most prediction programs have a setting to scan for TFBS for a given motif.
-   
-      **Example of mast commands:**
+For position weight matrices (PWM) or regular expressions we can use programs like MAST. 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).
+  
 {{{
-mast motif.txt  Sequence.fasta
-mast p53_BMC.txt  Promoters.fasta
- }}}
+mast MEME_motifs.txt Promoters.fasta
+}}}
+