RGT HINT differential --output-profiles

[EHowell1200]

Hey,

I noticed the --output-profiles option on HINT differential and it seemed perfect for what I was looking for. Well I ran it and the txt files produced for each motif only contain 1 row with the same data in the Lineplots folder txt files for each motif, seeming that it is just giving me the averaged score for all footprints, not for each instance as described. All 400+ motifs I have data for only contain a single row in the txt files and there is clearly more than 1 footprint instance for all these motifs. I included the command I ran below in case I am missing something. It would be nice to have the read scores for each footprint instance and the genomic coordinates so that I could specifically plot certain footprints (i.e. newly gained footprints/footprints only present in one condition for both samples)

Command:
rgt-hint differential --organism=mm10 --bc --nc 6 --mpbs-files=E9_1Runx1_fp_motif.bed,E9_Ctrl_fp_motif.bed --reads-files=E9_1Runx1.bam,E9_Ctrl.bam --conditions=E9_1Runx1,E9_Ctrl --output-location=E9_1Runx1_Ctrl_diff --output-profiles

[lzj1769]

Hi,

Thanks for reporting this issue.
I will try to fix it.

best,
Li