how to understand rgt-hint differential result

Question

[zq]

i am analysing an atac-seq data, when I run rgt-hint differential, I got the result successfully, but i have confuse about the result

for my understanding, as the official example showing, different sample show the different line significantly should be select as differential motif.

but see my top differential motifs.

why my result didnt show the difference in lineplot but with most significant pvalue

other motif without significant pvalue, but there is some difference in the plot

i used following command to run, can anyone help with this problem?

Am I make any mistake? or there is anyother issue?

rgt-hint footprinting --atac-seq --paired-end --organism=mm10 --output-location=./ \ --output-prefix=WT.merge.footprinting WT.merge.sort.modified.bam WT.Genrich.mod

rgt-hint footprinting --atac-seq --paired-end --organism=mm10 --output-location=./ \ --output-prefix=DKO.merge.footprinting DKO.merge.sort.modified.bam DKO.Genrich.mod

rgt-motifanalysis matching --organism=mm10 --input-files WT.merge.footprinting.bed DKO.merge.footprinting.bed

rgt-hint differential --organism=mm10 --bc --nc 24 \ --mpbs-files=./match/WT.merge.footprinting_mpbs.bed,./match/DKO.merge.footprinting_mpbs.bed \ --reads-files=WT.merge.sort.modified.bam,DKO.merge.sort.modified.bam \ --conditions=WT,DKO \ -output-location=WTvsDKO5

Answer 1

[angadmaurya311]

In my opinion, separation in line plot is heavily dependent on the number of Instance (Num, n=). Usually studies filter motifs below n=1000 for robust analysis.