Elementolab/GUI fire

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FIRE (motif analysis)

ChIPseeqer GUI: FIRE (motif analysis)
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ChIPseeqer GUI: FIRE (motif analysis)

How it works

1. Select the peaks file OR a folder that contains several peaks files.

2. Select the genome file.

3. Select the parameters of the program:

Species					choose the species of your data.

Random mode				select the mode to create random peaks. 
					(1) Completely random sequences on the same chromosome for each peak. 
					(2) Adjacent sequences to each peak. 
					(3) Using 1st order Markov model sequences learnt on peaks.

Use same seed for random regions	check this if you want to create random data from the same seed (makes comparison easier across runs)4

4. Press the button Run

5. This process will find the enriched motifs within your peaks, compared t motifs enriched in random regions.

6. The results (saved in the output files), are also shown in the Results tab.

ChIPseeqer GUI: FIRE results
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ChIPseeqer GUI: FIRE results

7. The equivalent command line tool is here

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