Screen tf motif within provided regions.
git clone git@github.com:zhoujj2013/motifpizza.gitEdit configuration at bin/config.txt Write the configure file, please refer to the format here.
perl $MotifInstallDir/ScanMotifWithBed.pl region.bed none tf.lst human out_prefix > log 2>errMotifpizza will store scanning result in out_prefix.all.motif.bed.
# chr start end motif_site_id score strand
chr1 7078860 7078878 Ahr_1 4.11009 +
chr1 7079079 7079097 Ahr_2 4.10092 +
chr1 12602157 12602175 Ahr_3 5.17431 +
chr1 13650235 13650253 Ahr_4 6.09174 +
chr1 16334792 16334810 Ahr_5 4.86239 -
chr1 20681581 20681599 Ahr_6 12.3853 +
chr1 20992263 20992281 Ahr_7 8.44954 -
chr1 20999204 20999222 Ahr_8 9.90826 +
chr1 20999339 20999357 Ahr_9 9.59633 -
chr1 21042468 21042486 Ahr_10 4.45872 +Motif source from:
http://genome.cshlp.org/content/26/3/385.full
Berger et al. 2008; Wei et al. 2010; Robasky and Bulyk 2011; Jolma et al. 2013; Mathelier et al. 2014
Charles E. Grant, Timothy L. Bailey, and William Stafford Noble, "FIMO: Scanning for occurrences of a given motif", Bioinformatics 27(7):1017–1018, 2011.
Saint-André, Violaine, et al. "Models of human core transcriptional regulatory circuitries." Genome research 26.3 (2016): 385-396.
Zhou, Jiajian, et al. "LncFunNet: an integrated computational framework for identification of functional long noncoding RNAs in mouse skeletal muscle cells." Nucleic acids research (2017).