how to understand rgt-hint differential result
1
0
Entering edit mode
4 months ago
zq • 0

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.

enter image description here

but see my top differential motifs. enter image description here enter image description here

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 enter image description here

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

rgt-hint atac command • 304 views
ADD COMMENT
1
Entering edit mode
4 months ago

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.

ADD COMMENT

Login before adding your answer.

Traffic: 1530 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6