findMotifs vs findMotifsGenome, inequality of results
so I'm testing
Homer for motif analysis. There are two tools
findMotifs.plwhich search motifs in "promoters" and also in provided
fastafiles (I don't want to use the
tssmode, because I want to analyze also intergenic features with this tool).
findMotifsGenome.plwhich search for motifs using preconfigured genome (
gtf) and sequences in
Both programs share majority of options, the main difference, as I see, is lack of
-size option in
Maybe it causes differences when analyzing the same sequences by both methods, here are my scripts:
findMotifs.pl peaks_factor/noctg_prom_ssc.fa zea findmotigs_ssc -fastaBg peaks_factor/noctg_prom_ss.fa -nomask -mset plants -mcheck ~/bin/homer/data/knownTFs/plants/all.motifs -mknown ~/bin/homer/data/knownTFs/plants/known.motifs -p 4 -fdr 100
findMotifsGenome.pl peaks_factor/noctg_prom_ssc.bed zm_v4old anal_homer_diff -bg peaks_factor/noctg_prom_ss.bed -h -size given -mcheck ~/bin/homer/data/knownTFs/plants/all.motifs -mknown ~/bin/homer/data/knownTFs/plants/known.motifs -nomask -p 4 -fdr 100
The output of
findMotifs.pl reports 732 "experimental" sequences and 293 control sequences.
findMotifsGenome.pl the corresponding values are 732 and 123.
I really don't know why..., as I have 732 "experimental" sequences and 338 control ones.
Both scripts give different results, does anyone have any experience with that scripts and can advice, which one is better?
Here is the link to documentation.
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