chen2meme [options]
Read a CHEN matrix file and convert to MEME format. You may concatenate files for more than one motif.
Reads concatenated CHEN files from standard input.
Concatenated CHEN files describe one or more motifs. Each motif has a header line and a position-weight matrix.
>NANOG
2 64 4 10
1 66 1 12
52 1 0 27
0 0 0 80
0 0 0 80
0 5 74 1
3 1 1 75
3 49 14 14
57 9 0 14
1 0 3 76
1 3 46 30
4 48 12 16
30 16 3 31
31 12 19 18
41 12 12 15
16 20 12 32
>OCT4
11 216 13 99
168 10 1 160
1 6 2 330
12 0 8 319
21 92 213 13
98 5 5 231
68 93 37 141
326 0 4 9
0 0 0 339
0 0 319 20
4 289 19 27
288 1 1 49
212 25 73 29
294 8 23 14
55 28 54 202
Writes MEME motif format to standard output.
A probability matrix and optionally a log-odds matrix are output for each motif in the file. The probability matrix is computed using pseudo-counts consisting of the background frequency (see -bg, below) multiplied by the total pseudocounts (see -pseudo, below). The log-odds matrix uses the background frequencies in the denominator and is log base 2.
| Option | Parameter | Description | Default Behaviour |
|---|---|---|---|
| General Options | |||
| -skip | ID | Skip the motif identified by ID. This option can be repeated to skip more than one motif. | Motifs are not skipped. |
| -bg | background file | The background file should be a Markov background model. It contains the background frequencies of letters use for assigning pseudocounts. The background frequencies will be included in the resulting MEME file. | Uses uniform background frequencies. |
| -pseudo | total pseudocounts | Add total pseudocounts times letter background to each frequency. | No pseudocount is added. |
| -logodds | Include a log-odds matrix in the output. This is not required for versions of the MEME Suite ≥ 4.7.0. | The log-odds matrix is not included in the output. | |
| -url | website | The provided website URL will be stored with the motif and this can be used by MEME Suite programs to provide a direct link to that information in their output. If website contains the keyword MOTIF_NAME the motif ID is substituted in place of MOTIF_NAME in the output. For example if the url is http://big-box-of-motifs.com/motifs/MOTIF_NAME.html and the motif ID is NANOG, the motif will contain a link to http://big-box-of-motifs.com/motifs/NANOG.html | The output does not include a URL with the motifs. |
| -h | Prints a usage message and exits. | The program runs as normal. | |