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Examples of how to use CREAD tools

Many examples can be found in the man pages. This page will be updated with additional examples.

formattable examples

Example files

These files may be used to try the examples below

example.mat example.lib

Example 1

matcompare -l example.lib -o output.factor \
example.mat

Compare motifs in example.mat with motifs in the library example.lib. Add an attribute to each input motif with the computed divergence between motifs in example.mat and example.lib

Example 2

matcompare -h 2 -t 1.5 -n 10 -l example.lib -o \
output.factor example.mat

Compare motifs in example.mat with motifs in the library example.lib. An overhang of 2 bases is allowed when comparing motifs, the threshold for similarity has been set at 1.5 and only the top 10 matches are printed for each motif in example.mat.

Example 3

matcompare -l example.lib -M -o output.factor \
example.mod

Compare the motifs comprising the modules in example.mod with motifs in the library example.lib.

Example 4

matcompare -a AlignmentFile -t 1.5 -l example.lib \
example.mat

The file AlignmentFile displays the alignment between the motifs pairs with divergence scores less than threshold 1.5.

Example 5

matcompare -L -t 1.5 -l example.lib \
example.mat

Compare motifs in example.mat to library of motifs example.lib and return results as a list of matching motifs.

Example 6

matcompare -C -t 0 -o output.factor -l example.lib \
example.mat

Compare the motifs in example.mat to those in example.lib using the chi squared test.

Example 7

matcompare -F -t 0 -o output.factor -l example.lib \
example.mat

Compare the motifs in example.mat to those in example.lib using the Fisher exact contingency table test.