Changes between Version 16 and Version 17 of SOPs/enriched_tf_binding_sites


Ignore:
Timestamp:
04/12/24 11:46:34 (9 months ago)
Author:
gbell
Comment:

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  • SOPs/enriched_tf_binding_sites

    v16 v17  
    88
    99==== MEME ====
    10 The [[http://meme-suite.org/tools/meme|MEME]] function of the [[http://meme-suite.org/index.html|MEME Suite]] uses expectation maximization (deterministic optimization) to perform de novo motif discovery from sequence input.  Spurious motifs can be reduced by filtering the input sequences, for example based on fold enrichment and/or reducing the sequence length (eg. ~200bp regions within the summit) from MACS for TFs in ChIP-Seq data.
     10The [[https://meme-suite.org/meme/tools/meme|MEME]] function of the [[http://meme-suite.org/index.html|MEME Suite]] uses expectation maximization (deterministic optimization) to perform de novo motif discovery from sequence input.  Spurious motifs can be reduced by filtering the input sequences, for example based on fold enrichment and/or reducing the sequence length (eg. ~200bp regions within the summit) from MACS for TFs in ChIP-Seq data.
    1111
    1212Sample commands:
    … …  
    7979Most 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.
    8080
    81 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:
     81MAST can be run using its web  [[https://meme-suite.org/meme/tools/mast]] or from the [[https://meme-suite.org/meme/doc/mast.html?man_type=web]] using one or more motifs in MEME format on a set of sequences like this:
    8282 
    8383{{{
    … …  
    8787When running from the command line, MAST will create a directory called mast_out where it places its output.
    8888
    89 FIMO can be run using its web  [[http://meme-suite.org/tools/fimo|interface]] or from the [[http://meme-suite.org/doc/fimo.html?man_type=command|command line]] using one or more motifs in MEME format on a set of sequences like this:
     89FIMO can be run using its web  [[https://meme-suite.org/meme/tools/fimo]] or from the [[https://meme-suite.org/meme/doc/fimo.html?man_type=web]] using one or more motifs in MEME format on a set of sequences like this:
    9090
    9191{{{