centrimo [options] <motif file> <sequence file>
CentriMo evaluates if motifs are centerally enriched in a set of sequences.
A file containing motifs. Outputs from MEME and DREME are supported along with minimal MEME format for which there are conversion scripts avaliable to support other formats. Input motifs that are likely to appear in the sequences.
A file containing FASTA formatted sequences which are expected to have the most interesing motifs appearing frequently in center. Typically this will be sequences centered on ChIP-seq peaks.
CentriMo outputs a text file called centrimo.txt which gives information on which motifs are most centrally enriched. If you have gnuplot installed it also creates a plot showing the output site probability curves for the top motifs. Additionally it creates the file site_counts.txt which can be used with centrimo-plots to regenerate the plots.
| Option | Parameter | Description | Default Behaviour |
|---|---|---|---|
| Input/Output | |||
| --o | <directory> | Create the directory and write output files in it. This option is not compatible with -oc as only one output directory is allowed. | The program behaves as if --oc centrimo_out had been specified. |
| --oc | <directory> | Create the directory but if it already exists allow overwriting the contents. This option is not compatible with --o as only one output directory is allowed. | The program behaves as if --oc centrimo_out had been specified. |
| --bgfile | <bg file> | Read a zero order background from the specified file. If motif-file is specified then read the background from the motif file. | The program uses the base frequencies in the input sequences. |
| Scanning | |||
| --seed | <seed> | Specify a number as the seed for initializing the pseudo-random number generator. | A seed of 0 is used. |
| --score | <S> | The score threshold for PWMs, in bits. Sequences without a site with score >= <S> are ignored. | A score of 5 is used. |
| Summarizing | |||
| --maxplots | <N> | Output site-probability curves for the <N> motifs with the
lowest central enrichment p-values on a single plot. Note: After running 'centrimo', you can use 'centrimo-plots' to remake plots and/or to make make separate plots for every motif. Type 'centrimo-plots -h' for more information. |
Up to 5 plots are combined. |
| Miscellaneous | |||
| -verbosity | <level> | A number that regulates the verbosity level of the output information messages. If set to 1 (quiet) then it will only output error messages whereas the other extreme 5 (dump) outputs lots of mostly useless information. | The verbosity level is set to 2 (normal). |