cp ~/Public_html/test/test1/knownResults/known5.motif .
cp ~/Public_html/test/test1/knownResults/known20.motif .
cp ../../LTR5B/LTR5B_homer_sort.bed .
awk '{split($1,a,"_"); $1=a[1]; print}' LTR5B_homer_sort.bed > LTR5B_homer_sort_clean.txt
awk 'BEGIN{OFS="\t"} {$1=$1; print}' LTR5B_homer_sort_clean.txt > LTR5B_homer_sort_clean.bed
bedtools getfasta -fi ../hg38.fa -bed LTR5B_homer_sort_clean.bed -fo LTR5B.fa -name -s
findMotifs.pl LTR5B.fa fasta homer_output/ -find known5.motif > AR_full_for_LTR5B.txt
findMotifs.pl LTR5B.fa fasta homer_output/ -find known20.motif > AR_half_for_LTR5B.txt