Usage:

centrimo [options] <primary sequence file> <motif file>+

Description

Input

Motif File(s)

File(s) containing MEME formatted motifs. Outputs from MEME and DREME are supported, as well as Minimal MEME Format. You can convert many other motif formats to MEME format using conversion scripts available with the MEME Suite.

Sequence File

A file containing FASTA formatted sequences, ideally all of the same length. The sequences in this file are referred to as the "primary sequences" when a second set of (control) sequences is provided using the --neg option (see below).

Output

CentriMo outputs an HTML file that allows interactive selection of which motifs to plot the positional distribution for and control over smoothing and other plotting parameters. CentriMo also outputs two text files: centrimo.txt, a tab delimited version of the results, and site_counts.txt, which lists, for each motif and each offset, the number of sequences where the best match of the motif occurs at the given offset.

Options

Option Parameter Description Default Behaviour
Input/Output
--negcontrol sequence file Plot the motif distributions in this set (the control sequences) as well.  
--disc   For each enriched region in the primary sequences, the signficance of the relative enrichment of the motif in that region in the primary versus control sequences is evaluated using Fisher's exact test. Requires the control sequences to be supplied with the --neg option. Use the binomial test on the primary sequences to evaluate motif enrichment.
--motif-pseudo pseudocount Add a this total pseudocount to the counts in each motif column when converting a frequency matrix to a log-odds score matrix. The pseudocount added to each count is pseudocount times the background frequency of the letter (see option --bfile, above). Note: Counts are computed from MEME formatted motifs by multiplying the the frequency of the letter times the value of nsites given in the motif letter-probability matrix header line. The program applies a pseudocount of 0.1.
--motif ID Select the motif with the ID for scanning. This option may be repeated to select multiple motifs. The program scans with all the motifs.
--seqlenlength Use sequences with the length length ignoring all other sequences in the input file(s). Use sequences with the same length as the first sequence, ignoring all other sequences in the input file(s).
Scanning
--score S The score threshold for PWMs, in bits. Sequences without a match with score ≥ S are ignored. A score of 5 is used.
--optimize_score  Search for the optimal score above the minimum threshold given by the --score option. The minimum score threshold is used.
--maxreg max region The maximum region size to consider. Try all region sizes up to the sequence width.
--minreg min region The minimum region size to consider. Must be less than max region. Try regions 1 bp and larger.
--norc   Do not scan with the reverse complement motif. Scans with the reverse complement motif.
--flip   reverse complement matches appear 'reflected' around sequence centers. Do not 'flip' the sequence; use rc of motif instead.
--local   Compute enrichment of all regions. Compute enrichment of central regions.
Output filtering
--ethresh thresh Limit the results to motifs with an enriched region whose E-value is less than thresh. Enrichment E-values are computed by first adjusting the binomial p-value of a region for the number of regions tested using the Bonferroni correction, and then multiplying the adjusted p-value by the number of motifs in the input to CentriMo. Include motifs with E-values up to 10.
Miscellaneous
--descdescription Include the text description in the HTML output. No description in the HTML output.
--dfiledesc file Include the first 500 characters of text from the file desc file in the HTML output. No description in the HTML output.
--noseq   Do not store sequence IDs in the output of CentriMo. CentriMo stores a list of the sequence IDs with matches in the best region for each motif. This can potentially make the file size much larger.
--version Display the version and exit. Run as normal.

Citing

If you use CentriMo in your research, please cite the following paper:
Timothy L. Bailey and Philip Machanick, "Inferring direct DNA binding from ChIP-seq", Nucleic Acids Research, 40:e128, 2012. [full text]