Changes between Version 9 and Version 10 of SOPs/enriched_tf_binding_sites


Ignore:
Timestamp:
11/04/20 14:39:17 (4 years ago)
Author:
gbell
Comment:

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  • SOPs/enriched_tf_binding_sites

    v9 v10  
    6161Depending on the source of the motif, the program used to scan for potential binding sites may be different.
    6262
    63 [http://www.biobase-international.com/wp-content/uploads/2012/03/Match_command_line.txt TRANSFAC's match] - for transcription factor binding sites
     63[http://gene-regulation.com/Match_command_line.txt TRANSFAC's match] - for transcription factor binding sites
    6464  * commercial application requiring a license for the most up-to-date version
    65   * Whitehead only: See BaRC_datasets/Transfac for the command-line program and data files
     65  * Whitehead only: See BaRC_datasets/Transfac for the command-line program and (old) data files
    6666{{{
    6767# Search using all Transfac profiles
    6868match matrix.dat MyPromoters.fa MyPromoters.match_out.txt minSUM_good.prf
     69
    6970# Search using a subset of profiles
    7071match matrix.dat MyPromoters.fa MyPromoters.vert.match_out.txt vertebrate_non_redundant_minSUM.prf