Changes between Version 4 and Version 5 of SOPs/enriched_tf_binding_sites

Timestamp:

05/13/16 14:59:28 (9 years ago)

Author:

gbell

Comment:

--

SOPs/enriched_tf_binding_sites

@@ -13 +13 @@
 
 {{{
-//meme testsmall.FA -oc TEST-OUT -dna // 
-//meme seq.fa -minw 6 -maxw 50 -mod oops //
+meme testsmall.FA -oc TEST-OUT -dna
+meme seq.fa -minw 6 -maxw 50 -mod oops
+# Look for 5 motifs of width 5-15, with 0 or 1 motifs per sequence expected
+meme Promoters.fa -dna -oc . -mod zoops -nmotifs 5 -minw 5 -maxw 15 -revcomp
 }}}
 
@@ -27 +29 @@
      anr     Any number
 }}}
+
+Tomtom can then be run to compare MEME motifs to database(s) of known motifs.  It's part of the MEME suite.
+
+{{{
+tomtom -no-ssc -oc . -verbosity 1 -min-overlap 5 -mi 1 -dist pearson -evalue -thresh 10.0 -o tomtom_out meme_out/meme.txt /nfs/BaRC_datasets/MEME_matrix_databases/Jaspar.meme.2016.txt /nfs/BaRC_datasets/MEME_matrix_databases/MotifDb.matrices.out.txt /nfs/BaRC_datasets/MEME_matrix_databases/Transfac_2014.1.dat.txt
+}}}
+
 ==== MEME-ChIP ====
 Motif Analysis of Large DNA Datasets. It is especially appropriate for analyzing the bound genomic regions identified in a transcription factor (TF) ChIP-seq experiment.  Note, MEME-ChIP pre-processes the data around the center of the region, "Prior to motif discovery and motif enrichment analysis, MEME-ChIP centers and trims each sequence to 100 bp; the full-length sequences are used in the subsequent motif visualization step." [[http://bioinformatics.oxfordjournals.org/content/27/12/1696.full | MEME-ChIP]]