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Motif-Finding

The goal for this project is to implement the known motif finding part of findMotifsGenome.pl from Homer in python.

More about the Homer motif analysis: http://homer.ucsd.edu/homer/motif/index.html

The project seprates into two parts: Part1: Read peak file, reference genome files, and motif library to generate motif matrix and Part2: Use motif matrix to generate the html report.

Set up

git clone https://github.com/HongjiZhu2001/Motif-Finding

cd Motif-Finding

pip install -r requirements.txt

If you encounter any errors with using seqlogo, you may also need to install Ghostscript: https://ghostscript.com/releases/gsdnld.html

Part1: Read peak file, reference genome files, and motif library to generate motif matrix

Usage: python Known_Motif_Search.py peak_file reference_genome_file output_file [optional]custom_motif_library

Example Usage:

python Known_Motif_Search.py peaks_Oct4.txt GRCm38.chr17.fa Oct4_known_motifs.txt

python Known_Motif_Search.py peaks_Sox2.txt GRCm38.chr17.fa Sox2_known_motifs.txt

python Known_Motif_Search.py peaks_Klf4.txt GRCm38.chr17.fa Klf4_known_motifs.txt Homer_motifs.txt

This repository contains the Homer motif library Homer_motifs.txt, from http://homer.ucsd.edu/homer/custom.motifs.

This repository also contains some example peak files of transcription factors: Oct4, Sox2, and Klf4: peaks_Oct4.txt, peaks_Sox2.txt, peaks_Klf4.txt

If no custom_motif_library is specified, the tool will use Homer_motifs.txt by default.

If you plan to use a custom_motif_library, please make sure it's in the same format as Homer_motifs.txt

Output: a motif_matrix_file containing the motifs found in the peak regions.

Part2: Use motif matrix to generate the html report

Usage: python HTML_Report.py motif_matrix_file [optional]output_file_name(out.html if not specified)

Example Usage:

python HTML_Report.py Oct4_known_motifs.txt Oct4_report

python HTML_Report.py Sox2_known_motifs.txt Sox2_report

python HTML_Report.py Klf4_known_motifs.txt Klf4_report

Output: a .html output containing the motif sequence found with the logo showing the probability of nucleotides.

For running data in More_Data folder:

Usage:

python Known_Motif_Search_Modified.py ./More_Data/.peak.bed_file GRCm38.chr17.fa output_file [optional]custom_motif_library

python HTML_Report_Modified.py motif_matrix_file(from previous step) output_file

Example Usage:

python Known_Motif_Search_Modified.py ./More_Data/ESC_Esrrb.peaks.bed GRCm38.chr17.fa Esrrb_known_motifs.txt

python HTML_Report_Modified.py Esrrb_known_motifs.txt Esrrb_report

References

Motif library:

http://homer.ucsd.edu/homer/motif/motifDatabase.html

http://homer.ucsd.edu/homer/custom.motifs

Data used for example usages:

https://www.ncbi.nlm.nih.gov/pubmed/28111071

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE90895