Differential motif enrichment | CentriMo | meme

两个peak set的motif差异富集

网页版更好用：https://meme-suite.org/meme/tools/centrimo

命令行需要准备文件，比较复杂。

wget https://jaspar.elixir.no/download/data/2024/CORE/JASPAR2024_CORE_vertebrates_non-redundant_pfms_meme.txt
ln -s /home/zz950/reference/refdata-gex-mm10-2020-A/fasta/genome.fa mm10.fasta
ln -s /home/zz950/reference/refdata-gex-GRCh38-2020-A/fasta/genome.fa hg38.fasta
ln -s /home/zz950/projects/BAF_SOX9/diffbind/motif_enrich/jaspar2meme_match/JASPAR2024.meme ./

bedtools getfasta -fi mm10.fasta -bed module.PROM1.pos.peaks.bed > module.PROM1.pos.peaks.fasta
bedtools getfasta -fi hg38.fasta -bed module.PROM1.neg.peaks.bed > module.PROM1.neg.peaks.fasta

# WRONG
# centrimo --oc diff_enrich_pos --neg module.PROM1.neg.peaks.fasta module.PROM1.pos.peaks.fasta JASPAR2024.meme

Parsing arguments
Arguments ok
Starting meme2alph
meme2alph motif_db/JASPAR/JASPAR2022_CORE_vertebrates_non-redundant_v2.meme alphabet.txt
meme2alph ran successfully in 0 seconds
Starting fasta-get-markov
fasta-get-markov -nostatus -nosummary -m 0 -alph alphabet.txt module.PROM1.neg.peaks.fasta module.PROM1.neg.peaks.fasta.bg
fasta-get-markov ran successfully in 0.01 seconds
Starting centrimo
centrimo --oc . --verbosity 1 --score 5.0 --ethresh 10.0 --bfile module.PROM1.neg.peaks.fasta.bg --neg module.PROM1.pos.peaks.fasta module.PROM1.neg.peaks.fasta motif_db/JASPAR/JASPAR2022_CORE_vertebrates_non-redundant_v2.meme
centrimo ran successfully in 44.84 seconds
Done

Parsing arguments
Arguments ok
Starting meme2alph
meme2alph motif_db/JASPAR/JASPAR2022_CORE_vertebrates_non-redundant_v2.meme alphabet.txt
meme2alph ran successfully in 0 seconds
Starting fasta-get-markov
fasta-get-markov -nostatus -nosummary -m 0 -alph alphabet.txt module.PROM1.pos.peaks.fasta module.PROM1.pos.peaks.fasta.bg
fasta-get-markov ran successfully in 0.01 seconds
Starting centrimo
centrimo --oc . --verbosity 1 --score 5.0 --ethresh 10.0 --bfile module.PROM1.pos.peaks.fasta.bg --neg module.PROM1.neg.peaks.fasta module.PROM1.pos.peaks.fasta motif_db/JASPAR/JASPAR2022_CORE_vertebrates_non-redundant_v2.meme
centrimo ran successfully in 44.49 seconds
Done