Elementolab/Find peaks with motif

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Find peaks with motif

This analysis can be followed after running Elementolab/ChIPseeqerFIRE and allows you to find the peaks that have a specific FIRE motif.

To run the tools directly from any folder, you need to add the $CHIPSEEQERDIR and $CHIPSEEQERDIR/SCRIPTS to your $PATH variable. Read How to set the CHIPSEEQERDIR variable.

1. Type the command:

perl SCRIPTS/find_peaks_with_motif.pl --targets=your_FIRE_folder/DNA/TF_targets_15_FIRE.txt --seed=motif
-targets=FILE	Point to the peaks files that is located under your FIRE_results/DNA/ directory
-seed=STR	Can be any of the seeds found in your FIRE results. E.g., CCCGCCC, ATTCTTA (the available seeds can be found in the .summary.pdf file -see image below)
-fromfile=STR  Point to a peaks file. The script will retrieve the peaks with motif that are also present in this file. This can be helpful when multiple categories are used in FIRE
Example of FIRE output
Enlarge
Example of FIRE output

2. See the results.

The output of the script is a your_FIRE_folder/DNA/TF_targets_15_FIRE.txt.CCCGCCC.txt.

3. What can I do next ?

Once you get a list of peaks saved in a text file, you can:

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