Homer forecast motif

HOMER:Software for motif discovery and ChIP-Seq analysis.

Homer yes motif Discovery and ChIP-Seq Analysis software

1. from FASTA Find... In the file motif

## conda install homer

### 1. from FASTA Find... In the file motif
findMotifs.pl <targetSequences.fa> fasta <output directory> -fasta <background.fa> [options] -find motif1.motif > outputfile.txt

homer2 denovo -i input.fa -b background.fa > outputfile.txt

2. From the promoter region of the gene set motif

### 2.  From the promoter region of the gene set motif
##  You need to download relevant data first 
#  lookup 
perl /home/zheng/miniconda3/envs/chip_seq/share/homer/.//configureHomer.pl -list

#  Install first 
perl /home/zheng/miniconda3/envs/chip_seq/share/homer/.//configureHomer.pl -install human-p
perl /home/zheng/miniconda3/envs/chip_seq/share/homer/.//configureHomer.pl -install hg38

findMotifs.pl homer_geneID.txt human out -start -800 -end 200 -p 32
nohup findMotifs.pl homer_geneID.txt human out -start -800 -end 200 &

3. Found in genomic regions motif

### 3. Found in genomic regions motif
findMotifsGenome.pl test_peaks.xls /home/ref/seq/hg38.fa peakAnalysis -size 200 -len 8 -p 50

findMotifsGenome.pl test_peaks.xls human-p peakAnalysis -size 200 -len 8 -p 50

#  Long running time 
#  Be careful ：test_peaks.xls come from Mac2 result , Reference genome fasta file location /home/ref/seq/hg38.fa 
#  The script run will be established at the location of the reference genome preparsed Folder 
#  Parameter description ：
# -size:fragment size to use for motif finding
# -len:motif length

HOMER It can also be used for various enrichment analysis

Reference resources ：

http://homer.ucsd.edu/homer/microarray/index.html
http://homer.ucsd.edu/homer/