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rajanil / msCentipede

A hierarchical multiscale model for inferring transcription factor binding from chromatin accessibility data.
MIT License
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Help with interpreting plot_accessibility_profile.py output #20

Open lucygarner opened 4 years ago

lucygarner commented 4 years ago

Hi,

From running plot_accessibility_profile.py for the TF Rorgt, I am getting the following plot: image

I have ATAC-seq data (three replicate BAM files) and the Rorgt motif sites were identified using scanMotifGenomeWide.pl from HOMER.

Could someone help me with interpreting this please? I can't see the grey line which is supposed to represent the profile at unbound sites?

This is the footprint I got for CTCF, but I still don't see the line for unbound motifs: image

Many thanks, Lucy